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]
moretodo = true
interrupted = false
- # check if the pipeline os owned by a group
- owner_uuid = nil
- group_result = $client.execute(:api_method => $arvados.groups.get,
- :parameters => {
- :uuid => @instance[:owner_uuid]
- },
- :authenticated => false,
- :headers => {
- authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
- })
- group = JSON.parse group_result.body, :symbolize_names => true
- if group[:uuid]
- owner_uuid = group[:uuid]
- end
-
+ 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,
+ :runtime_constraints => c[:runtime_constraints],
:owner_uuid => owner_uuid,
# TODO: Delete the following three attributes when
# supporting pre-20140418 API servers is no longer
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
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
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
- elsif c[:job][:success] == false
+ elsif c[:job][:success] == false or c[:job][:cancelled_at]
failed += 1
end
end
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[:state] = 'Complete'
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