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.
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).
: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 to 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)
stop_on [:'--']
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."
abort
end
-if $options[:run_here] == $options[:submit]
- abort "#{$0}: syntax error: you must supply either --run-here or --submit."
+if $options[:run_pipeline_here] == $options[:submit]
+ abort "#{$0}: error: you must supply --run-pipeline-here, --run-jobs-here, or --submit."
end
# Suppress SSL certificate checks if ARVADOS_API_HOST_INSECURE
# Set up the API client.
-$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)
end
def self.create(attributes)
result = $client.execute(:api_method => $arvados.pipeline_instances.create,
- :body => {
+ :body_object => {
:pipeline_instance => attributes
},
:authenticated => false,
})
j = JSON.parse result.body, :symbolize_names => true
unless j.is_a? Hash and j[:uuid]
- abort "Failed to create pipeline_instance: #{j[:errors] rescue nil} #{j.inspect}"
+ 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)
:parameters => {
:uuid => @pi[:uuid]
},
- :body => {
- :pipeline_instance => @attributes_to_update.to_json
+ :body_object => {
+ :pipeline_instance => @attributes_to_update
},
:authenticated => false,
:headers => {
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 = {}
[]
end
end
- def self.create(job, create_params)
+ def self.create(pipeline, component, job, create_params)
@cache ||= {}
- jsonified_create_params = {}
- create_params.each do |k, v|
- jsonified_create_params[k] = v.to_json unless v.nil?
- end
+ body = {job: no_nil_values(job)}.merge(no_nil_values(create_params))
result = $client.execute(:api_method => $arvados.jobs.create,
- :body => {
- :job => job.to_json
- }.merge(jsonified_create_params),
+ :body_object => body,
:authenticated => false,
:headers => {
authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
if j.is_a? Hash and j[:uuid]
@cache[j[:uuid]] = j
else
- debuglog "create job: #{j[:errors] rescue nil} with attributes #{job}", 0
+ debuglog "create job: #{j[:errors] rescue nil} with attributes #{body}", 0
+
+ msg = ""
+ j[: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)
nil
end
end
+
+ protected
+
+ def self.no_nil_values(hash)
+ hash.reject { |key, value| value.nil? }
+ end
end
class WhRunPipelineInstance
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 => {
param = params_args.shift.sub /^--/, ''
params[param] = params_args.shift
else
- abort "Syntax error: I do not know what to do with arg \"#{params_args[0]}\""
+ 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|
end
end
if !errors.empty?
- abort "Errors:\n#{errors.collect { |c,p,e| "#{c}::#{p} - #{e}\n" }.join ""}"
+ abort "\n#{Time.now} -- pipeline_template #{@template[:uuid]}\nErrors:\n#{errors.collect { |c,p,e| "#{c}::#{p} - #{e}\n" }.join ""}"
end
debuglog "options=" + @options.pretty_inspect
self
end
def setup_instance
- if $options[:submit]
- @instance ||= PipelineInstance.
- create(:components => @components,
- :pipeline_template_uuid => @template[:uuid],
- :state => 'New')
+ if @instance
+ @instance[:properties][:run_options] ||= {}
+ if @options[:no_reuse]
+ # override properties of existing instance
+ @instance[:properties][:run_options][:enable_job_reuse] = false
+ else
+ # Default to "enable reuse" if not specified. (This code path
+ # can go away when old clients go away.)
+ if @instance[:properties][:run_options][:enable_job_reuse].nil?
+ @instance[:properties][:run_options][:enable_job_reuse] = true
+ end
+ end
else
- @instance ||= PipelineInstance.
- create(:components => @components,
- :pipeline_template_uuid => @template[:uuid],
- :state => 'RunningOnClient')
+ @instance = PipelineInstance.
+ create(components: @components,
+ properties: {
+ run_options: {
+ enable_job_reuse: !@options[:no_reuse]
+ }
+ },
+ pipeline_template_uuid: @template[:uuid],
+ state: ($options[:submit] ? 'RunningOnServer' : 'RunningOnClient'))
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
# 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({
+ 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_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,
}, {
# 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]),
+ :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)
else
debuglog "component #{cname} new job failed", 0
job_creation_failed += 1
end
end
+ if c[:job] and c[:run_in_process]
+ 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: {
+ finished_at: Time.now,
+ running: false,
+ success: false
+ })
+ end
+ end
+
if c[:job] and c[:job][:uuid]
if (c[:job][:running] or
not (c[:job][:finished_at] or c[:job][:cancelled_at]))
# 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]}"
+
+ debuglog "names: #{@instance[:name]} #{@template[:name]}", 0
+ if (not @instance[:name].nil?) and (not @instance[:name].empty?)
+ pipeline_name = @instance[:name]
+ else
+ fetch_template(@instance[:pipeline_template_uuid])
+ pipeline_name = @template[:name]
+ 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 = $arv.link.create link: \
- {
- link_class: 'resources',
- name: 'wants',
- tail_kind: 'arvados#user',
- tail_uuid: @my_user_uuid,
- head_kind: 'arvados#collection',
- head_uuid: wanted,
- owner_uuid: owner_uuid
- }
- debuglog "added link, uuid #{newlink[:uuid]}"
+ debuglog "Could not find a collection with portable data hash #{portable_data_hash}", 0
end
end
end
end
end
+ if @instance[:finished_at].nil? and ['Complete', 'Failed'].include? @instance[:state]
+ @instance[:finished_at] = Time.now
+ end
+
debuglog "pipeline instance state is #{@instance[:state]}"
# set components_summary
"failed #{c[:job][:finished_at]}"
elsif c[:job][:started_at]
"started #{c[:job][:started_at]}"
+ elsif c[:job][:is_locked_by_uuid]
+ "starting #{c[:job][:started_at]}"
else
"queued #{c[:job][:created_at]}"
end
end
end
end
+
+ def abort(msg)
+ if @instance
+ if ["New", "Ready", "RunningOnClient",
+ "RunningOnServer"].include?(@instance[:state])
+ @instance[:state] = "Failed"
+ @instance[:finished_at] = Time.now
+ @instance.save
+ end
+ @instance.log_stderr(msg)
+ end
+ Kernel::abort(msg)
+ end
end
runner = WhRunPipelineInstance.new($options)
projects / arvados.git / blobdiff