# == Synopsis
#
-# wh-run-pipeline-instance --template pipeline-template-uuid [options] [--] [parameters]
-# wh-run-pipeline-instance --instance pipeline-instance-uuid [options]
+# 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.
#
# [--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
#
-# [--create-only] Do not try to satisfy any components. Just create an
-# instance, print its UUID to stdout, and exit.
+# [--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
abort "#{$0}: fatal: ARVADOS_API_TOKEN environment variable not set."
begin
+ require 'arvados'
require 'rubygems'
- require 'google/api_client'
require 'json'
require 'pp'
require 'trollop'
-rescue LoadError
+ require 'google/api_client'
+rescue LoadError => l
+ puts $:
abort <<-EOS
-#{$0}: fatal: some runtime dependencies are missing.
-Try: gem install pp google-api-client json trollop
+#{$0}: fatal: #{l.message}
+Some runtime dependencies may be missing.
+Try: gem install arvados pp google-api-client json trollop
EOS
end
# this program, that is, not the pipeline component parameters).
p = Trollop::Parser.new do
+ version __FILE__
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,
"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)
:short => :none,
:type => :integer)
opt(:template,
- "UUID of pipeline 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(:create_only,
+ opt(:submit,
"Do not try to satisfy any components. Just create a pipeline instance and output its UUID.",
:short => :none,
:type => :boolean)
+ opt(:run_here,
+ "Manage the pipeline in process.",
+ :short => :none,
+ :type => :boolean)
stop_on [:'--']
end
$options = Trollop::with_standard_exception_handling p do
$debuglevel = $options[:debug_level] || ($options[:debug] && 1) || 0
if $options[:instance]
- if $options[:template] or $options[:create_only]
- abort "#{$0}: syntax error: --instance cannot be combined with --template or --create-only."
+ if $options[:template] or $options[:submit]
+ abort "#{$0}: syntax error: --instance cannot be combined with --template or --submit."
end
elsif not $options[:template]
abort "#{$0}: syntax error: you must supply a --template or --instance."
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 }
+end
+
# Set up the API client.
$client ||= Google::APIClient.
: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'
class PipelineInstance
def self.find(uuid)
result = $client.execute(:api_method => $arvados.pipeline_instances.get,
:parameters => {
- :api_token => ENV['ARVADOS_API_TOKEN'],
:uuid => uuid
},
+ :body => {
+ :api_token => ENV['ARVADOS_API_TOKEN']
+ },
:authenticated => false)
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,
- :parameters => {
+ :body => {
:api_token => ENV['ARVADOS_API_TOKEN'],
- :pipeline_instance => attributes.to_json
+ :pipeline_instance => attributes
},
:authenticated => false)
j = JSON.parse result.body, :symbolize_names => true
def save
result = $client.execute(:api_method => $arvados.pipeline_instances.update,
:parameters => {
+ :uuid => @pi[:uuid]
+ },
+ :body => {
:api_token => ENV['ARVADOS_API_TOKEN'],
- :uuid => @pi[:uuid],
:pipeline_instance => @attributes_to_update.to_json
},
:authenticated => false)
[]
end
end
- def self.create(attributes)
+ def self.create(job, create_params)
@cache ||= {}
result = $client.execute(:api_method => $arvados.jobs.create,
:parameters => {
:api_token => ENV['ARVADOS_API_TOKEN'],
- :job => attributes.to_json
- },
+ :job => job.to_json
+ }.merge(create_params),
:authenticated => false)
j = JSON.parse result.body, :symbolize_names => true
if j.is_a? Hash and j[:uuid]
@cache[j[:uuid]] = j
else
- debuglog "create job: #{j[:errors] rescue nil}"
+ debuglog "create job: #{j[:errors] rescue nil} with attributes #{job}", 0
nil
end
end
@options = _options
end
- def fetch_template(template_uuid)
- result = $client.execute(:api_method => $arvados.pipeline_templates.get,
- :parameters => {
- :api_token => ENV['ARVADOS_API_TOKEN'],
- :uuid => template_uuid
- },
- :authenticated => false)
- @template = JSON.parse result.body, :symbolize_names => true
- if !@template[:uuid]
- abort "#{$0}: fatal: failed to retrieve pipeline template #{template_uuid} #{@template[:errors].inspect rescue nil}"
+ 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
+ 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 => {
+ :api_token => ENV['ARVADOS_API_TOKEN'],
+ :uuid => template
+ },
+ :authenticated => false)
+ @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
params_args.shift if params_args[0] == '--'
params = {}
while !params_args.empty?
- if (re = params_args[0].match /^(--)?([^-].*?)=(.)/)
+ if (re = params_args[0].match /^(--)?([^-].*?)=(.+)/)
params[re[2]] = re[3]
params_args.shift
elsif params_args.size > 1
end
def setup_instance
- @instance ||= PipelineInstance.
- create(:components => @components,
+ if $options[:submit]
+ @instance ||= PipelineInstance.
+ create(:components => @components,
+ :pipeline_template_uuid => @template[:uuid],
+ :state => 'New')
+ else
+ @instance ||= PipelineInstance.
+ create(:components => @components,
:pipeline_template_uuid => @template[:uuid],
- :active => true)
+ :state => 'RunningOnClient')
+ end
self
end
def run
moretodo = true
+ interrupted = false
+
while moretodo
moretodo = false
@components.each do |cname, c|
job = nil
+ # 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] &&
+ !c[:job][:success].nil?)
if !c[:job] and
- c[:script_parameters].select { |pname, p| p.is_a? Hash }.empty?
- # Job is fully specified (all parameter values are present) but
- # no particular job has been found.
-
- debuglog "component #{cname} ready to satisfy."
-
- c.delete :wait
- second_place_job = nil # satisfies component, but not finished yet
- JobCache.where(:script => c[:script],
- :script_parameters => c[:script_parameters],
- :script_version_descends_from => c[:script_version_descends_from]).
- each do |candidate_job|
- candidate_params_downcase = Hash[candidate_job[:script_parameters].
- map { |k,v| [k.downcase,v] }]
- c_params_downcase = Hash[c[:script_parameters].
- map { |k,v| [k.downcase,v] }]
-
- debuglog "component #{cname} considering job #{candidate_job[:uuid]} version #{candidate_job[:script_version]} parameters #{candidate_params_downcase.inspect}", 3
-
- unless candidate_params_downcase == c_params_downcase
- next
- end
-
- unless candidate_job[:success] || candidate_job[:running] ||
- (!candidate_job[:started_at] && !candidate_job[:cancelled_at])
- debuglog "component #{cname} would be satisfied by job #{candidate_job[:uuid]} if it were running or successful.", 2
- next
- end
-
- if candidate_job[:success]
- job = candidate_job
- debuglog "component #{cname} satisfied by job #{job[:uuid]} version #{job[:script_version]}"
- c[:job] = job
- else
- second_place_job ||= candidate_job
- end
- break
- end
- if not c[:job] and second_place_job
- job = second_place_job
- debuglog "component #{cname} satisfied by job #{job[:uuid]} version #{job[:script_version]}"
+ 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({
+ :script => c[:script],
+ :script_parameters => c[:script_parameters],
+ :script_version => c[:script_version],
+ :repository => c[:repository],
+ :nondeterministic => c[:nondeterministic],
+ :output_is_persistent => c[:output_is_persistent] || false,
+ # TODO: Delete the following three attributes when
+ # supporting pre-20140418 API servers is no longer
+ # important. New API servers take these as flags that
+ # control behavior of create, rather than job attributes.
+ :minimum_script_version => c[:minimum_script_version],
+ :exclude_script_versions => c[:exclude_minimum_script_versions],
+ :no_reuse => @options[:no_reuse] || c[:nondeterministic],
+ }, {
+ # 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 => !(@options[:no_reuse] || c[:nondeterministic]),
+ })
+ if job
+ debuglog "component #{cname} new job #{job[:uuid]}"
c[:job] = job
+ else
+ debuglog "component #{cname} new job failed"
end
- if not c[:job]
- debuglog "component #{cname} not satisfied by any existing job."
- if !@options[:dry_run]
- debuglog "component #{cname} new job."
- job = JobCache.create(:script => c[:script],
- :script_parameters => c[:script_parameters],
- :resource_limits => c[:resource_limits] || {},
- :script_version => c[:script_version] || 'master')
- if job
- debuglog "component #{cname} new job #{job[:uuid]}"
- c[:job] = job
- else
- debuglog "component #{cname} new job failed: #{job[:errors]}"
- end
- end
- end
- else
- c[:wait] = true
end
+
if c[:job] and c[:job][:uuid]
- if not c[:job][:finished_at] and not c[:job][:cancelled_at]
+ if (c[:job][:running] or
+ not (c[:job][:finished_at] or c[:job][:cancelled_at]))
+ # Job is running so update copy of job record
c[:job] = JobCache.get(c[:job][:uuid])
end
+
if c[:job][:success]
# Populate script_parameters of other components waiting for
# this job
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]
+ 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 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]}"
+ 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
+ }
+ debuglog "added link, uuid #{newlink[:uuid]}"
end
end
end
elsif c[:job][:running] ||
(!c[:job][:started_at] && !c[:job][:cancelled_at])
- moretodo ||= !@options[:no_wait]
+ # Job is still running
+ moretodo = true
elsif c[:job][:cancelled_at]
debuglog "component #{cname} job #{c[:job][:uuid]} cancelled."
end
end
end
@instance[:components] = @components
- @instance[:active] = moretodo
report_status
- sleep 10 if moretodo
+
+ if @options[:no_wait]
+ moretodo = false
+ end
+
+ if moretodo
+ begin
+ sleep 10
+ rescue Interrupt
+ debuglog "interrupt", 0
+ interrupted = true
+ break
+ end
+ end
+ end
+
+ ended = 0
+ succeeded = 0
+ failed = 0
+ @components.each do |cname, c|
+ if c[:job]
+ if c[:job][:finished_at]
+ ended += 1
+ if c[:job][:success] == true
+ succeeded += 1
+ elsif c[:job][:success] == false
+ failed += 1
+ end
+ end
+ end
end
- @instance[:success] = @components.reject { |cname,c| c[:job] and c[:job][:success] }.empty?
+
+ success = (succeeded == @components.length)
+
+ 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
+
+ # 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
- @instance[:active] = false
+ if @instance and @instance[:state] == 'RunningOnClient'
+ @instance[:state] = 'Paused'
@instance.save
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|
end
runner.apply_parameters(p.leftovers)
runner.setup_instance
- if $options[:create_only]
+ if $options[:submit]
runner.instance.save
puts runner.instance[:uuid]
else
projects / arvados.git / blobdiff