scout-gear 7.2.0 → 8.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/.vimproject +51 -6
- data/VERSION +1 -1
- data/bin/scout +6 -3
- data/lib/rbbt-scout.rb +1 -0
- data/lib/scout/cmd.rb +1 -1
- data/lib/scout/concurrent_stream.rb +33 -29
- data/lib/scout/config.rb +1 -1
- data/lib/scout/exceptions.rb +1 -0
- data/lib/scout/log/color.rb +4 -2
- data/lib/scout/log/progress/report.rb +1 -1
- data/lib/scout/log/progress/util.rb +71 -2
- data/lib/scout/log/progress.rb +1 -1
- data/lib/scout/log/trap.rb +107 -0
- data/lib/scout/log.rb +56 -21
- data/lib/scout/meta_extension.rb +13 -6
- data/lib/scout/misc/digest.rb +1 -1
- data/lib/scout/misc/format.rb +12 -0
- data/lib/scout/misc/helper.rb +31 -0
- data/lib/scout/misc/insist.rb +1 -1
- data/lib/scout/misc/monitor.rb +12 -1
- data/lib/scout/misc/system.rb +10 -0
- data/lib/scout/misc.rb +1 -0
- data/lib/scout/named_array.rb +65 -3
- data/lib/scout/open/lock/lockfile.rb +587 -0
- data/lib/scout/open/lock.rb +28 -2
- data/lib/scout/open/remote.rb +4 -0
- data/lib/scout/open/stream.rb +111 -42
- data/lib/scout/open/util.rb +13 -3
- data/lib/scout/path/find.rb +9 -1
- data/lib/scout/path/util.rb +35 -0
- data/lib/scout/persist/serialize.rb +18 -5
- data/lib/scout/persist.rb +60 -30
- data/lib/scout/resource/path.rb +53 -0
- data/lib/scout/resource/produce.rb +0 -8
- data/lib/scout/resource/util.rb +2 -1
- data/lib/scout/semaphore.rb +8 -1
- data/lib/scout/tmpfile.rb +7 -8
- data/lib/scout/tsv/attach.rb +177 -0
- data/lib/scout/tsv/change_id.rb +40 -0
- data/lib/scout/tsv/dumper.rb +85 -54
- data/lib/scout/tsv/index.rb +188 -20
- data/lib/scout/tsv/open.rb +182 -0
- data/lib/scout/tsv/parser.rb +200 -118
- data/lib/scout/tsv/path.rb +5 -6
- data/lib/scout/tsv/persist/adapter.rb +26 -37
- data/lib/scout/tsv/persist/fix_width_table.rb +327 -0
- data/lib/scout/tsv/persist/serialize.rb +117 -0
- data/lib/scout/tsv/persist/tokyocabinet.rb +6 -3
- data/lib/scout/tsv/persist.rb +4 -2
- data/lib/scout/tsv/transformer.rb +141 -0
- data/lib/scout/tsv/traverse.rb +136 -37
- data/lib/scout/tsv/util/filter.rb +312 -0
- data/lib/scout/tsv/util/process.rb +73 -0
- data/lib/scout/tsv/util/reorder.rb +81 -0
- data/lib/scout/tsv/util/select.rb +265 -0
- data/lib/scout/tsv/util/unzip.rb +86 -0
- data/lib/scout/tsv/util.rb +126 -19
- data/lib/scout/tsv.rb +28 -5
- data/lib/scout/work_queue/socket.rb +6 -1
- data/lib/scout/work_queue/worker.rb +5 -2
- data/lib/scout/work_queue.rb +15 -8
- data/lib/scout/workflow/definition.rb +29 -2
- data/lib/scout/workflow/step/dependencies.rb +24 -4
- data/lib/scout/workflow/step/info.rb +40 -5
- data/lib/scout/workflow/step/progress.rb +14 -0
- data/lib/scout/workflow/step/provenance.rb +8 -7
- data/lib/scout/workflow/step/status.rb +45 -0
- data/lib/scout/workflow/step.rb +104 -33
- data/lib/scout/workflow/task/inputs.rb +14 -20
- data/lib/scout/workflow/task.rb +86 -47
- data/lib/scout/workflow/usage.rb +10 -6
- data/scout-gear.gemspec +30 -3
- data/scout_commands/workflow/task +37 -9
- data/scout_commands/workflow/task_old +2 -2
- data/test/scout/open/test_stream.rb +61 -59
- data/test/scout/path/test_find.rb +10 -1
- data/test/scout/resource/test_produce.rb +15 -0
- data/test/scout/test_meta_extension.rb +25 -0
- data/test/scout/test_named_array.rb +18 -0
- data/test/scout/test_persist.rb +67 -0
- data/test/scout/test_tmpfile.rb +1 -1
- data/test/scout/test_tsv.rb +222 -3
- data/test/scout/test_work_queue.rb +21 -18
- data/test/scout/tsv/persist/test_adapter.rb +11 -1
- data/test/scout/tsv/persist/test_fix_width_table.rb +134 -0
- data/test/scout/tsv/persist/test_tokyocabinet.rb +29 -1
- data/test/scout/tsv/test_attach.rb +227 -0
- data/test/scout/tsv/test_change_id.rb +98 -0
- data/test/scout/tsv/test_dumper.rb +1 -1
- data/test/scout/tsv/test_index.rb +127 -3
- data/test/scout/tsv/test_open.rb +167 -0
- data/test/scout/tsv/test_parser.rb +45 -3
- data/test/scout/tsv/test_persist.rb +9 -0
- data/test/scout/tsv/test_transformer.rb +108 -0
- data/test/scout/tsv/test_traverse.rb +195 -3
- data/test/scout/tsv/test_util.rb +24 -0
- data/test/scout/tsv/util/test_filter.rb +188 -0
- data/test/scout/tsv/util/test_process.rb +47 -0
- data/test/scout/tsv/util/test_reorder.rb +94 -0
- data/test/scout/tsv/util/test_select.rb +58 -0
- data/test/scout/tsv/util/test_unzip.rb +112 -0
- data/test/scout/work_queue/test_socket.rb +0 -1
- data/test/scout/work_queue/test_worker.rb +63 -6
- data/test/scout/workflow/step/test_load.rb +3 -3
- data/test/scout/workflow/step/test_status.rb +31 -0
- data/test/scout/workflow/task/test_inputs.rb +14 -14
- data/test/scout/workflow/test_step.rb +13 -13
- data/test/scout/workflow/test_task.rb +168 -32
- data/test/scout/workflow/test_usage.rb +33 -6
- data/test/test_helper.rb +3 -1
- metadata +29 -2
@@ -21,38 +21,6 @@ class TestTask < Test::Unit::TestCase
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assert_equal 2, s.run
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end
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def test_override_inputs
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wf = Workflow.annonymous_workflow "TaskInputs" do
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input :input1, :string
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task :step1 => :string do |i| i end
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dep :step1, :input1 => 1
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input :input2, :string
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task :step2 => :string do |i| i end
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end
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job = wf.job(:step2, :input1 => 2)
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assert_equal Task::DEFAULT_NAME, job.name
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assert_not_equal Task::DEFAULT_NAME, job.step(:step1).name
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end
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def test_override_inputs_block
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wf = Workflow.annonymous_workflow "TaskInputs" do
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input :input1, :string
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task :step1 => :string do |i| i end
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dep :step1 do |id,options|
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{:inputs => {:input1 => 1}}
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end
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input :input2, :string
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task :step2 => :string do |i| i end
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end
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job = wf.job(:step2, :input1 => 2)
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assert_equal Task::DEFAULT_NAME, job.name
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assert_not_equal Task::DEFAULT_NAME, job.step(:step1).name
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end
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def test_task_override_dep
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wf = Workflow.annonymous_workflow "TaskInputs" do
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input :input1, :integer
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assert_equal Task::DEFAULT_NAME, job.name
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step1 = wf.job(:step1, :input1 => 3)
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assert_equal 3, step1.run
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job = wf.job(:double, "TaskInputs#step1" => step1)
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assert_equal 12, job.run
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assert_not_equal Task::DEFAULT_NAME, job.name
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step1 = wf.job(:step1, :input1 => 4)
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assert_equal 4, step1.run
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job = wf.job(:double, "TaskInputs#step1" => step1)
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assert_equal 14, job.run
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assert_not_equal Task::DEFAULT_NAME, job.name
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job = wf.job(:my_sum, :vv1 => 2, :vv2 => 3)
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assert_equal 5, job.run
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end
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def test_defaults_in_dep_block
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wf = Workflow.annonymous_workflow "TaskInputs" do
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input :v1, :integer
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input :v2, :integer
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task :sum => :integer do |v1,v2|
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v1 + v2
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end
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input :vv1, :integer
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input :vv2, :integer, nil, 3
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dep :sum, :v1 => :placeholder, :v2 => :placeholder do |jobname,options,dependencies|
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raise "Non-numeric value where integer expected" unless Numeric === options[:vv1]
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{inputs: {v1: options[:vv1], v2: options[:vv2]} }
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end
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task :my_sum => :integer do
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dependencies.last.load
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end
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end
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job = wf.job(:my_sum, :vv1 => "2")
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assert_equal 5, job.run
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end
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def test_dependency_jobname
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wf = Workflow.annonymous_workflow "TaskInputs" do
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input :v1, :integer
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input :v2, :integer
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task :sum => :integer do |v1,v2|
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v1 + v2
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end
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input :vv1, :integer
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input :vv2, :integer
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dep :sum, :v1 => :vv1, :v2 => :vv2, :jobname => "OTHER_NAME"
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task :my_sum => :integer do
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dependencies.last.load
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end
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end
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job = wf.job(:my_sum, "TEST_NAME", :vv1 => 2, :vv2 => 3)
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assert_equal 5, job.run
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assert_equal "TEST_NAME", job.clean_name
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assert_equal "OTHER_NAME", job.step(:sum).clean_name
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end
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def test_no_param_last_job
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wf = Workflow.annonymous_workflow "TaskInputs" do
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input :v1, :integer
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input :v2, :integer
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task :sum => :integer do |v1,v2|
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v1 + v2
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end
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dep :sum
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task :my_sum => :integer do
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dependencies.last.load
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end
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end
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job = wf.job(:my_sum, :v1 => 2, :v2 => "3")
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assert_equal 5, job.run
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refute_equal Task::DEFAULT_NAME, job.name
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end
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def test_no_param_last_job_block
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wf = Workflow.annonymous_workflow "TaskInputs" do
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input :v1, :integer
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input :v2, :integer
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task :sum => :integer do |v1,v2|
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v1 + v2
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end
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dep :sum do |jobname,options|
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{inputs: options}
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end
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task :my_sum => :integer do
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dependencies.last.load
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end
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end
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job = wf.job(:my_sum, :v1 => 2, :v2 => "3")
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assert_equal 5, job.run
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refute_equal Task::DEFAULT_NAME, job.name
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end
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def test_override_inputs_block
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wf = Workflow.annonymous_workflow "TaskInputs" do
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input :input1, :string
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task :step1 => :string do |i| i end
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dep :step1, :input1 => 1 do |id,options|
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{:inputs => options}
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end
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input :input2, :string
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task :step2 => :string do |i| step(:step1).load end
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end
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job = wf.job(:step2, :input1 => 2)
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assert_equal 1, job.run
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assert_equal Task::DEFAULT_NAME, job.name
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assert_not_equal Task::DEFAULT_NAME, job.step(:step1).name
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end
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def test_override_inputs_block_array
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wf = Workflow.annonymous_workflow "TaskInputs" do
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input :input1, :string
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task :step1 => :string do |i| i end
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dep :step1, :input1 => 1 do |id,options|
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[{:inputs => options}]
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end
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input :input2, :string
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task :step2 => :string do |i| step(:step1).load end
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end
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job = wf.job(:step2, :input1 => 2)
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assert_equal 1, job.run
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assert_equal Task::DEFAULT_NAME, job.name
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assert_not_equal Task::DEFAULT_NAME, job.step(:step1).name
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end
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def test_override_inputs
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wf = Workflow.annonymous_workflow "TaskInputs" do
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input :input1, :string
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task :step1 => :string do |i| i end
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dep :step1, :input1 => 1
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input :input2, :string
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task :step2 => :string do |i| step(:step1).load end
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end
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job = wf.job(:step2, :input1 => 2)
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assert_equal 1, job.run
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assert_equal Task::DEFAULT_NAME, job.name
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assert_not_equal Task::DEFAULT_NAME, job.step(:step1).name
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end
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def test_non_default_inputs
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wf = Workflow.annonymous_workflow "TaskInputs" do
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input :input1, :integer, "", 1
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input :input2, :integer, "", 0
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task :step1 => :string do |i1,i2| i1 + i2 end
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dep :step1, :input2 => 1
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task :step2 => :string do |i| step(:step1).load end
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dep :step2
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task :step3 => :string do |i| step(:step1).load end
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end
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job = wf.job(:step3, :input1 => 1)
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assert_equal Task::DEFAULT_NAME, job.name
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assert_not_equal Task::DEFAULT_NAME, job.step(:step1).name
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assert_equal 2, job.run
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job = wf.job(:step3, :input1 => 2)
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assert_equal 3, job.run
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job = wf.job(:step3)
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assert_equal Task::DEFAULT_NAME, job.name
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assert_not_equal Task::DEFAULT_NAME, job.step(:step1).name
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end
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end
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self.name = "UsageWorkflow"
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self.title = "Workflow to test documentation"
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self.description = "Use this workflow to
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self.description = "Use this workflow to evaluate if the documentation is correctly presented."
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desc "Desc"
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input :array, :array, "Array"
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task :step1 => :string do
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task :step1 => :string do |a|
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a * ", "
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end
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dep :step1
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desc "Desc2"
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dep :step1
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input :float, :float, "Float"
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task :step2 => :string do |f|
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step(:step1).load + " " + f.to_s
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end
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desc "Desc2_fixed"
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dep :step1, :array => %w(a b)
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input :float, :float, "Float"
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task :
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task :step2_fixed => :string do
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end
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desc 'Desc3'
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task_alias :step3, UsageWorkflow, :step2
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desc "Desc3"
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dep :step3, :array => %w(a b)
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task :step3_fixed => :string do
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end
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end
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def test_workflow_usage
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assert_match "
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assert_match "evaluate if the documentation", UsageWorkflow.usage
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end
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def test_task_usage
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assert_match
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|
+
assert_match /Desc2/, UsageWorkflow.tasks[:step2].usage(UsageWorkflow)
|
49
|
+
assert_match /--array/, UsageWorkflow.tasks[:step2].usage(UsageWorkflow)
|
50
|
+
assert_match /Desc2_fixed/, UsageWorkflow.tasks[:step2_fixed].usage(UsageWorkflow)
|
51
|
+
assert_match /Desc3/, UsageWorkflow.tasks[:step3].usage(UsageWorkflow)
|
52
|
+
assert_match /--array/, UsageWorkflow.tasks[:step3].usage(UsageWorkflow)
|
53
|
+
end
|
54
|
+
|
55
|
+
def test_task_input_fixed
|
56
|
+
assert_match /Desc2_fixed/, UsageWorkflow.tasks[:step2_fixed].usage(UsageWorkflow)
|
57
|
+
refute_match /--array/, UsageWorkflow.tasks[:step2_fixed].usage(UsageWorkflow)
|
58
|
+
assert_match /Desc3/, UsageWorkflow.tasks[:step3_fixed].usage(UsageWorkflow)
|
59
|
+
refute_match /--array/, UsageWorkflow.tasks[:step3_fixed].usage(UsageWorkflow)
|
33
60
|
end
|
34
61
|
end
|
35
62
|
|
data/test/test_helper.rb
CHANGED
@@ -33,12 +33,14 @@ class Test::Unit::TestCase
|
|
33
33
|
end
|
34
34
|
|
35
35
|
def tmpdir
|
36
|
-
@tmpdir
|
36
|
+
@tmpdir ||= Path.setup('tmp/test_tmpdir').find
|
37
37
|
end
|
38
38
|
|
39
39
|
setup do
|
40
|
+
TmpFile.tmpdir = tmpdir.tmpfiles
|
40
41
|
Log::ProgressBar.default_severity = 0
|
41
42
|
Persist.cache_dir = tmpdir.var.cache
|
43
|
+
Persist::MEMORY_CACHE.clear
|
42
44
|
Open.remote_cache_dir = tmpdir.var.cache
|
43
45
|
Workflow.directory = tmpdir.var.jobs
|
44
46
|
Workflow.workflows.each{|wf| wf.directory = Workflow.directory[wf.name] }
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: scout-gear
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version:
|
4
|
+
version: 8.0.0
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2023-05-
|
11
|
+
date: 2023-05-23 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: term-ansicolor
|
@@ -114,17 +114,20 @@ files:
|
|
114
114
|
- lib/scout/log/progress.rb
|
115
115
|
- lib/scout/log/progress/report.rb
|
116
116
|
- lib/scout/log/progress/util.rb
|
117
|
+
- lib/scout/log/trap.rb
|
117
118
|
- lib/scout/meta_extension.rb
|
118
119
|
- lib/scout/misc.rb
|
119
120
|
- lib/scout/misc/digest.rb
|
120
121
|
- lib/scout/misc/filesystem.rb
|
121
122
|
- lib/scout/misc/format.rb
|
123
|
+
- lib/scout/misc/helper.rb
|
122
124
|
- lib/scout/misc/insist.rb
|
123
125
|
- lib/scout/misc/monitor.rb
|
124
126
|
- lib/scout/misc/system.rb
|
125
127
|
- lib/scout/named_array.rb
|
126
128
|
- lib/scout/open.rb
|
127
129
|
- lib/scout/open/lock.rb
|
130
|
+
- lib/scout/open/lock/lockfile.rb
|
128
131
|
- lib/scout/open/remote.rb
|
129
132
|
- lib/scout/open/stream.rb
|
130
133
|
- lib/scout/open/util.rb
|
@@ -152,15 +155,26 @@ files:
|
|
152
155
|
- lib/scout/simple_opt/setup.rb
|
153
156
|
- lib/scout/tmpfile.rb
|
154
157
|
- lib/scout/tsv.rb
|
158
|
+
- lib/scout/tsv/attach.rb
|
159
|
+
- lib/scout/tsv/change_id.rb
|
155
160
|
- lib/scout/tsv/dumper.rb
|
156
161
|
- lib/scout/tsv/index.rb
|
162
|
+
- lib/scout/tsv/open.rb
|
157
163
|
- lib/scout/tsv/parser.rb
|
158
164
|
- lib/scout/tsv/path.rb
|
159
165
|
- lib/scout/tsv/persist.rb
|
160
166
|
- lib/scout/tsv/persist/adapter.rb
|
167
|
+
- lib/scout/tsv/persist/fix_width_table.rb
|
168
|
+
- lib/scout/tsv/persist/serialize.rb
|
161
169
|
- lib/scout/tsv/persist/tokyocabinet.rb
|
170
|
+
- lib/scout/tsv/transformer.rb
|
162
171
|
- lib/scout/tsv/traverse.rb
|
163
172
|
- lib/scout/tsv/util.rb
|
173
|
+
- lib/scout/tsv/util/filter.rb
|
174
|
+
- lib/scout/tsv/util/process.rb
|
175
|
+
- lib/scout/tsv/util/reorder.rb
|
176
|
+
- lib/scout/tsv/util/select.rb
|
177
|
+
- lib/scout/tsv/util/unzip.rb
|
164
178
|
- lib/scout/work_queue.rb
|
165
179
|
- lib/scout/work_queue/socket.rb
|
166
180
|
- lib/scout/work_queue/worker.rb
|
@@ -173,7 +187,9 @@ files:
|
|
173
187
|
- lib/scout/workflow/step/file.rb
|
174
188
|
- lib/scout/workflow/step/info.rb
|
175
189
|
- lib/scout/workflow/step/load.rb
|
190
|
+
- lib/scout/workflow/step/progress.rb
|
176
191
|
- lib/scout/workflow/step/provenance.rb
|
192
|
+
- lib/scout/workflow/step/status.rb
|
177
193
|
- lib/scout/workflow/task.rb
|
178
194
|
- lib/scout/workflow/task/inputs.rb
|
179
195
|
- lib/scout/workflow/usage.rb
|
@@ -234,19 +250,30 @@ files:
|
|
234
250
|
- test/scout/test_work_queue.rb
|
235
251
|
- test/scout/test_workflow.rb
|
236
252
|
- test/scout/tsv/persist/test_adapter.rb
|
253
|
+
- test/scout/tsv/persist/test_fix_width_table.rb
|
237
254
|
- test/scout/tsv/persist/test_tokyocabinet.rb
|
255
|
+
- test/scout/tsv/test_attach.rb
|
256
|
+
- test/scout/tsv/test_change_id.rb
|
238
257
|
- test/scout/tsv/test_dumper.rb
|
239
258
|
- test/scout/tsv/test_index.rb
|
259
|
+
- test/scout/tsv/test_open.rb
|
240
260
|
- test/scout/tsv/test_parser.rb
|
241
261
|
- test/scout/tsv/test_persist.rb
|
262
|
+
- test/scout/tsv/test_transformer.rb
|
242
263
|
- test/scout/tsv/test_traverse.rb
|
243
264
|
- test/scout/tsv/test_util.rb
|
265
|
+
- test/scout/tsv/util/test_filter.rb
|
266
|
+
- test/scout/tsv/util/test_process.rb
|
267
|
+
- test/scout/tsv/util/test_reorder.rb
|
268
|
+
- test/scout/tsv/util/test_select.rb
|
269
|
+
- test/scout/tsv/util/test_unzip.rb
|
244
270
|
- test/scout/work_queue/test_socket.rb
|
245
271
|
- test/scout/work_queue/test_worker.rb
|
246
272
|
- test/scout/workflow/step/test_dependencies.rb
|
247
273
|
- test/scout/workflow/step/test_info.rb
|
248
274
|
- test/scout/workflow/step/test_load.rb
|
249
275
|
- test/scout/workflow/step/test_provenance.rb
|
276
|
+
- test/scout/workflow/step/test_status.rb
|
250
277
|
- test/scout/workflow/task/test_inputs.rb
|
251
278
|
- test/scout/workflow/test_definition.rb
|
252
279
|
- test/scout/workflow/test_documentation.rb
|