X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/aad2f86f509b34f1507bd5530bc458daf14feb41..548e0c54db524cb7317850d4dfd8f3ee0b93cdb0:/sdk/cli/bin/arv-run-pipeline-instance diff --git a/sdk/cli/bin/arv-run-pipeline-instance b/sdk/cli/bin/arv-run-pipeline-instance index 0adfc83fc7..6dc82c5a20 100755 --- a/sdk/cli/bin/arv-run-pipeline-instance +++ b/sdk/cli/bin/arv-run-pipeline-instance @@ -1,61 +1,5 @@ #!/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. -# class WhRunPipelineInstance end @@ -65,12 +9,6 @@ if RUBY_VERSION < '1.9.3' then 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' @@ -79,7 +17,7 @@ begin require 'trollop' require 'google/api_client' rescue LoadError => l - puts $: + $stderr.puts $: abort <<-EOS #{$0}: fatal: #{l.message} Some runtime dependencies may be missing. @@ -91,28 +29,33 @@ def debuglog(message, verbosity=1) $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 - - # 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(< :boolean, @@ -166,6 +109,14 @@ p = Trollop::Parser.new do "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 @@ -181,7 +132,7 @@ if $options[:instance] 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 @@ -190,22 +141,6 @@ if $options[:run_pipeline_here] == $options[:submit] abort "#{$0}: error: you must supply --run-pipeline-here, --run-jobs-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. $arv = Arvados.new api_version: 'v1' @@ -220,7 +155,7 @@ class PipelineInstance }, :authenticated => false, :headers => { - authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN'] + authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN'] }) j = JSON.parse result.body, :symbolize_names => true unless j.is_a? Hash and j[:uuid] @@ -238,7 +173,7 @@ class PipelineInstance }, :authenticated => false, :headers => { - authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN'] + authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN'] }) j = JSON.parse result.body, :symbolize_names => true unless j.is_a? Hash and j[:uuid] @@ -257,7 +192,7 @@ class PipelineInstance }, :authenticated => false, :headers => { - authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN'] + authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN'] }) j = JSON.parse result.body, :symbolize_names => true unless j.is_a? Hash and j[:uuid] @@ -301,7 +236,7 @@ class JobCache }, :authenticated => false, :headers => { - authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN'] + authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN'] }) @cache[uuid] = JSON.parse result.body, :symbolize_names => true end @@ -313,7 +248,7 @@ class JobCache }, :authenticated => false, :headers => { - authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN'] + authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN'] }) list = JSON.parse result.body, :symbolize_names => true if list and list[:items].is_a? Array @@ -331,7 +266,7 @@ class JobCache :body_object => body, :authenticated => false, :headers => { - authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN'] + authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN'] }) j = JSON.parse result.body, :symbolize_names => true if j.is_a? Hash and j[:uuid] @@ -375,7 +310,7 @@ class WhRunPipelineInstance }, :authenticated => false, :headers => { - authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN'] + authorization: 'OAuth2 '+$arv.config['ARVADOS_API_TOKEN'] }) @template = JSON.parse result.body, :symbolize_names => true if !@template[:uuid] @@ -439,12 +374,17 @@ class WhRunPipelineInstance if value.nil? and ![false,'false',0,'0'].index parameter[:required] if parameter[:output_of] + if not @components[parameter[:output_of].intern] + errors << [componentname, parametername, "output_of refers to nonexistent component '#{parameter[:output_of]}'"] + end next end errors << [componentname, parametername, "required parameter is missing"] 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? @@ -468,15 +408,23 @@ class WhRunPipelineInstance 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 @@ -500,7 +448,7 @@ class WhRunPipelineInstance # 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 @@ -509,7 +457,9 @@ class WhRunPipelineInstance my_submit_id = "instance #{@instance[:uuid]} rand #{rand(2**64).to_s(36)}" job = 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], @@ -517,6 +467,7 @@ class WhRunPipelineInstance :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. @@ -537,7 +488,7 @@ class WhRunPipelineInstance end end - if c[:job] and c[:run_in_process] + if c[:job] and c[:run_in_process] and not ["Complete", "Failed", "Cancelled"].include? c[:job][:state] report_status begin require 'open3' @@ -566,28 +517,25 @@ class WhRunPipelineInstance debuglog "Interrupted (#{e}). Failing job.", 0 $arv.job.update(uuid: c[:job][:uuid], job: { - finished_at: Time.now, - running: false, - success: false + 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 @@ -645,12 +593,15 @@ class WhRunPipelineInstance 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 @@ -677,21 +628,12 @@ class WhRunPipelineInstance 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) @@ -757,20 +699,18 @@ class WhRunPipelineInstance @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]}" - elsif c[:job][:is_locked_by_uuid] - "starting #{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