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."
+ puts "error: you must supply a --template or --instance."
+ p.educate
+ abort
end
if $options[:run_here] == $options[:submit]
:parameters => {
:uuid => uuid
},
- :body => {
- :api_token => ENV['ARVADOS_API_TOKEN']
- },
- :authenticated => false)
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['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
def self.create(attributes)
result = $client.execute(:api_method => $arvados.pipeline_instances.create,
:body => {
- :api_token => ENV['ARVADOS_API_TOKEN'],
:pipeline_instance => attributes
},
- :authenticated => false)
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
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}"
:uuid => @pi[:uuid]
},
:body => {
- :api_token => ENV['ARVADOS_API_TOKEN'],
:pipeline_instance => @attributes_to_update.to_json
},
- :authenticated => false)
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['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
@cache ||= {}
result = $client.execute(:api_method => $arvados.jobs.get,
:parameters => {
- :api_token => ENV['ARVADOS_API_TOKEN'],
:uuid => uuid
},
- :authenticated => false)
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['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 => {
- :api_token => ENV['ARVADOS_API_TOKEN'],
:limit => 10000,
:where => conditions.to_json
},
- :authenticated => false)
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+ })
list = JSON.parse result.body, :symbolize_names => true
if list and list[:items].is_a? Array
list[:items]
def self.create(job, create_params)
@cache ||= {}
result = $client.execute(:api_method => $arvados.jobs.create,
- :parameters => {
- :api_token => ENV['ARVADOS_API_TOKEN'],
+ :body => {
:job => job.to_json
}.merge(create_params),
- :authenticated => false)
+ :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]
@cache[j[:uuid]] = j
else
result = $client.execute(:api_method => $arvados.pipeline_templates.get,
:parameters => {
- :api_token => ENV['ARVADOS_API_TOKEN'],
:uuid => template
},
- :authenticated => false)
+ :authenticated => false,
+ :headers => {
+ authorization: 'OAuth2 '+ENV['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}"
if $options[:submit]
@instance ||= PipelineInstance.
create(:components => @components,
- :pipeline_template_uuid => @template[:uuid])
+ :pipeline_template_uuid => @template[:uuid],
+ :state => 'New')
else
@instance ||= PipelineInstance.
create(:components => @components,
moretodo = true
interrupted = false
+ 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")
:repository => c[:repository],
:nondeterministic => c[:nondeterministic],
:output_is_persistent => c[:output_is_persistent] || false,
+ :owner_uuid => owner_uuid,
# TODO: Delete the following three attributes when
# supporting pre-20140418 API servers is no longer
# important. New API servers take these as flags that
debuglog "component #{cname} new job #{job[:uuid]}"
c[:job] = job
else
- debuglog "component #{cname} new job failed"
+ debuglog "component #{cname} new job failed", 0
+ job_creation_failed += 1
end
end
tail_kind: 'arvados#user',
tail_uuid: @my_user_uuid,
head_kind: 'arvados#collection',
- head_uuid: wanted
+ head_uuid: wanted,
+ owner_uuid: owner_uuid
}
debuglog "added link, uuid #{newlink[:uuid]}"
end
end
end
@instance[:components] = @components
- @instance[:active] = moretodo
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
debuglog "interrupt", 0
interrupted = true
break
- #abort
end
end
end
failed = 0
@components.each do |cname, c|
if c[:job]
- if c[:job][:finished_at]
+ 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
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[:active] = false
- @instance[:success] = success
- @instance[:state] = "Complete"
+ @instance[:state] = 'Complete'
else
- @instance[:active] = nil
- @instance[:success] = nil
@instance[:state] = 'Paused'
end
else
if ended == @components.length or failed > 0
- @instance[:active] = false
- @instance[:success] = success
- @instance[:state] = success ? "Complete" : "Failed"
+ @instance[:state] = success ? 'Complete' : 'Failed'
end
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
end
def cleanup
- if @instance
- @instance[:active] = false
+ if @instance and @instance[:state] == 'RunningOnClient'
+ @instance[:state] = 'Paused'
@instance.save
end
end
projects / arvados.git / blobdiff