def refresh_todo
@todo = Job.queue
+ @todo_pipelines = PipelineInstance.queue
end
def sinfo
raise "No CRUNCH_JOB_BIN env var, and crunch-job not in path."
end
+ require 'shellwords'
+
+ arvados_internal = Rails.configuration.git_internal_dir
+ if not File.exists? arvados_internal
+ $stderr.puts `mkdir -p #{arvados_internal.shellescape} && cd #{arvados_internal.shellescape} && git init --bare`
+ end
+
+ src_repo = File.join(Rails.configuration.git_repositories_dir, job.repository + '.git')
+ src_repo = File.join(Rails.configuration.git_repositories_dir, job.repository, '.git') unless File.exists? src_repo
+
+ unless src_repo
+ $stderr.puts "dispatch: #{File.join Rails.configuration.git_repositories_dir, job.repository} doesn't exist"
+ sleep 1
+ untake(job)
+ next
+ end
+
+ $stderr.puts `cd #{arvados_internal.shellescape} && git fetch --no-tags #{src_repo.shellescape} && git tag #{job.uuid.shellescape} #{job.script_version.shellescape}`
+
cmd_args << crunch_job_bin
cmd_args << '--job-api-token'
cmd_args << job_auth.api_token
cmd_args << '--job'
cmd_args << job.uuid
-
- commit = Commit.where(sha1: job.script_version).first
- if commit
- cmd_args << '--git-dir'
- if File.exists?(File.
- join(Rails.configuration.git_repositories_dir,
- commit.repository_name + '.git'))
- cmd_args << File.
- join(Rails.configuration.git_repositories_dir,
- commit.repository_name + '.git')
- else
- cmd_args << File.
- join(Rails.configuration.git_repositories_dir,
- commit.repository_name, '.git')
- end
- end
+ cmd_args << '--git-dir'
+ cmd_args << arvados_internal
$stderr.puts "dispatch: #{cmd_args.join ' '}"
job_done = j_done[:job]
$stderr.puts "dispatch: child #{pid_done} exit"
$stderr.puts "dispatch: job #{job_done.uuid} end"
- $redis.publish job_done.uuid, "end"
# Ensure every last drop of stdout and stderr is consumed
read_pipes
# Wait the thread
j_done[:wait_thr].value
+ jobrecord = Job.find_by_uuid(job_done.uuid)
+ jobrecord.running = false
+ jobrecord.finished_at ||= Time.now
+ # Don't set 'jobrecord.success = false' because if the job failed to run due to an
+ # issue with crunch-job or slurm, we want the job to stay in the queue.
+ jobrecord.save!
+
# Invalidate the per-job auth token
j_done[:job_auth].update_attributes expires_at: Time.now
+ $redis.publish job_done.uuid, "end"
+
@running.delete job_done.uuid
end
+ def update_pipelines
+ expire_tokens = @pipe_auth_tokens.dup
+ @todo_pipelines.each do |p|
+ pipe_auth = (@pipe_auth_tokens[p.uuid] ||= ApiClientAuthorization.
+ create(user: User.where('uuid=?', p.modified_by_user_uuid).first,
+ api_client_id: 0))
+ puts `export ARVADOS_API_TOKEN=#{pipe_auth.api_token} && arv-run-pipeline-instance --run-here --no-wait --instance #{p.uuid}`
+ expire_tokens.delete p.uuid
+ end
+
+ expire_tokens.each do |k, v|
+ v.update_attributes expires_at: Time.now
+ @pipe_auth_tokens.delete k
+ end
+ end
+
def run
act_as_system_user
@running ||= {}
+ @pipe_auth_tokens ||= { }
$stderr.puts "dispatch: ready"
while !$signal[:term] or @running.size > 0
read_pipes
unless @todo.empty? or did_recently(:start_jobs, 1.0) or $signal[:term]
start_jobs
end
+ unless (@todo_pipelines.empty? and @pipe_auth_tokens.empty?) or did_recently(:update_pipelines, 5.0)
+ update_pipelines
+ end
end
reap_children
select(@running.values.collect { |j| [j[:stdout], j[:stderr]] }.flatten,