workflow_manager 0.2.6 → 0.2.7
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- data/lib/workflow_manager/server.rb +34 -26
- data/lib/workflow_manager/version.rb +1 -1
- data/spec/server_spec.rb +14 -2
- metadata +1 -1
@@ -134,16 +134,16 @@ module WorkflowManager
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end
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def input_dataset_tsv_path(script_content)
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gstore_dir = nil
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-
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+
input_dataset_path = nil
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script_content.split(/\n/).each do |line|
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if line =~ /GSTORE_DIR=(.+)/
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gstore_dir = $1.chomp
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elsif line =~ /INPUT_DATASET=(.+)/
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-
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+
input_dataset_path = $1.chomp
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break
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end
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end
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-
[gstore_dir,
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+
[gstore_dir, input_dataset_path]
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end
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def input_dataset_file_list(dataset_tsv_path)
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file_list = []
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@@ -163,6 +163,7 @@ module WorkflowManager
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flag = false
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break
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end
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p file
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end
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flag
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end
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@@ -207,34 +208,41 @@ module WorkflowManager
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def start_monitoring2(script_path, script_content, user='sushi_lover', project_number=0, sge_options='', log_dir='')
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# script_path is only used to generate a log file name
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# It is not used to read the script contents
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-
gstore_dir,
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if gstore_dir and
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-
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file_list
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-
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gstore_dir, input_dataset_path = input_dataset_tsv_path(script_content)
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if gstore_dir and input_dataset_path
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file_list = input_dataset_file_list(input_dataset_path)
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file_list.map!{|file| File.join(gstore_dir, file)}
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waiting_max = 60*60*8 # 8h
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#waiting_max = 60*3 # 3m
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worker = Thread.new(0, file_list, log_dir, script_path, script_content, sge_options) do |waiting_time, file_list, log_dir, script_path, script_content, sge_options|
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# wait until the files come
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-
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-
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-
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-
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until waiting_time > waiting_max or go_submit = input_dataset_exist?(file_list)
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p file_list
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sleep @interval
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waiting_time += @interval
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end
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-
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-
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-
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-
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-
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job_id, log_file, command = if go_submit
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@cluster.submit_job(script_path, script_content, sge_options)
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end
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if job_id and log_file
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# job status check until it finishes with success or fail
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loop do
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# check status
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current_status = check_status(job_id, log_file)
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-
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-
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# save time and status
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update_time_status(job_id, current_status, script_path, user, project_number)
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-
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-
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# finalize (kill current thred) in case of success or fail
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finalize_monitoring(current_status, log_file, log_dir)
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-
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-
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-
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-
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-
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# wait
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sleep @interval
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end # loop
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end # if
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job_id
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end # Thread
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end
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end
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def start_monitoring(submit_command, user = 'sushi lover', resubmit = 0, script = '', project_number = 0, sge_options='', log_dir = '')
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data/spec/server_spec.rb
CHANGED
@@ -54,7 +54,7 @@ describe Server do
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GSTORE_DIR=/srv/gstore/projects
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INPUT_DATASET=/srv/gstore/projects/p1535/test_masa/input_dataset.tsv"
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}
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-
let(:path){
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+
let(:path){
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[
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'/srv/gstore/projects',
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'/srv/gstore/projects/p1535/test_masa/input_dataset.tsv'
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@@ -80,12 +80,24 @@ INPUT_DATASET=/srv/gstore/projects/p1535/test_masa/input_dataset.tsv"
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it {is_expected.to be_nil}
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end
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context 'when submit_job successed' do
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pending
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=begin
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let(:waiting_time){0}
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before do
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allow(cluster).to receive(:submit_job).and_return(['job_id', 'log_file', 'command'])
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-
allow(Thread).to receive(:new)
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allow(Thread).to receive(:new).and_yield('log_file', 'log_dir', 'script_path', waiting_time)
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allow(server).to receive(:input_dataset_exist?).and_return(true)
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allow(cluster).to receive(:submit_job).and_return('job_id', 'log_file','command')
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allow(server).to receive(:check_status)
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allow(server).to receive(:update_time_status)
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allow(server).to receive(:finalize_monitoring)
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end
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subject {server.start_monitoring2(script_path, script_content)}
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it {is_expected.to eq 'job_id'}
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=end
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end
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context 'when input dataset does not exist' do
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pending
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end
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end
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describe '#success_or_fail' do
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