rbbt-util 5.29.0 → 5.30.1
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/lib/rbbt/hpc/orchestrate.rb +96 -8
- data/lib/rbbt/hpc/slurm.rb +57 -24
- data/lib/rbbt/persist.rb +4 -0
- data/lib/rbbt/persist/tsv/adapter.rb +44 -13
- data/lib/rbbt/tsv.rb +6 -2
- data/lib/rbbt/util/cmd.rb +6 -1
- data/lib/rbbt/util/misc/inspect.rb +13 -3
- data/lib/rbbt/util/misc/options.rb +0 -42
- data/lib/rbbt/util/procpath.rb +49 -0
- data/lib/rbbt/workflow/accessor.rb +6 -1
- data/lib/rbbt/workflow/step/accessor.rb +20 -13
- data/lib/rbbt/workflow/step/dependencies.rb +1 -2
- data/lib/rbbt/workflow/step/run.rb +2 -5
- data/lib/rbbt/workflow/usage.rb +1 -1
- data/lib/rbbt/workflow/util/provenance.rb +5 -2
- data/share/rbbt_commands/slurm/clean +165 -0
- data/share/rbbt_commands/slurm/list +174 -95
- data/share/rbbt_commands/slurm/orchestrate +3 -2
- data/share/rbbt_commands/slurm/task +1 -0
- data/share/rbbt_commands/tsv/slice +3 -3
- data/share/rbbt_commands/workflow/info +1 -1
- data/share/rbbt_commands/workflow/task +27 -7
- data/share/rbbt_commands/workflow/write_info +52 -0
- data/test/rbbt/test_workflow.rb +7 -7
- data/test/rbbt/util/test_procpath.rb +23 -0
- metadata +7 -2
data/test/rbbt/test_workflow.rb
CHANGED
@@ -386,9 +386,9 @@ class TestWorkflow < Test::Unit::TestCase
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386
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job.run
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387
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Misc.with_env "RBBT_UPDATE", 'true' do
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388
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assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
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389
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-
job = TestWF.job(:t3)
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390
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-
job.step(:t1).clean
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391
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-
assert job.checks.select{|d| d.task_name.to_s == "t1" }.empty?
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389
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+
#job = TestWF.job(:t3)
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390
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+
#job.step(:t1).clean
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391
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+
#assert job.checks.select{|d| d.task_name.to_s == "t1" }.empty?
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job = TestWF.job(:t3).recursive_clean
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job.run
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assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
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@@ -427,7 +427,7 @@ class TestWorkflow < Test::Unit::TestCase
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TmpFile.with_file do |dir|
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Path.setup(dir)
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Step.save_job_inputs(job, dir)
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430
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-
assert_equal Dir.glob(dir + "/*"), [dir.file.find + '.
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+
assert_equal Dir.glob(dir + "/*"), [dir.file.find + '.yaml']
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inputs = Workflow.load_inputs(dir, [:file], :file => :file)
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assert_equal inputs, {:file => 'code'}
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end
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@@ -455,9 +455,9 @@ class TestWorkflow < Test::Unit::TestCase
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job.run
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Misc.with_env "RBBT_UPDATE", 'true' do
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assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
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458
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-
job = TestWF.job(:t3)
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459
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-
job.step(:t1).clean
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460
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-
assert job.checks.select{|d| d.task_name.to_s == "t1" }.empty?
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458
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+
#job = TestWF.job(:t3)
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#job.step(:t1).clean
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#assert job.checks.select{|d| d.task_name.to_s == "t1" }.empty?
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job = TestWF.job(:t3).recursive_clean
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job.run
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assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
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@@ -0,0 +1,23 @@
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1
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+
require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
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require 'rbbt/util/procpath'
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+
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class TestProcPath < Test::Unit::TestCase
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def test_record_and_plot
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Log.with_severity 0 do
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pid = Process.fork do
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a = ""
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(0..1000).each do
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a << (0..rand(10000).to_i).to_a.collect{|i| "TEST #{i}" } * " "
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sleep 0.1
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end
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end
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TmpFile.with_file(nil, false) do |db|
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ProcPath.record(pid, db, :interval => '1', "recnum" => 100)
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ProcPath.plot(db, db + '.svg', "moving-average-window" => 1 )
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end
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end
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end
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end
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+
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
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name: rbbt-util
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version: !ruby/object:Gem::Version
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-
version: 5.
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+
version: 5.30.1
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platform: ruby
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authors:
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- Miguel Vazquez
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2021-
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+
date: 2021-02-02 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rake
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@@ -300,6 +300,7 @@ files:
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- lib/rbbt/util/misc/system.rb
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- lib/rbbt/util/named_array.rb
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- lib/rbbt/util/open.rb
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+
- lib/rbbt/util/procpath.rb
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- lib/rbbt/util/python.rb
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- lib/rbbt/util/semaphore.rb
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- lib/rbbt/util/simpleDSL.rb
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@@ -378,6 +379,7 @@ files:
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- share/rbbt_commands/resource/produce
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- share/rbbt_commands/resource/read
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- share/rbbt_commands/rsync
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382
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+
- share/rbbt_commands/slurm/clean
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- share/rbbt_commands/slurm/list
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- share/rbbt_commands/slurm/orchestrate
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- share/rbbt_commands/slurm/task
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@@ -437,6 +439,7 @@ files:
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- share/rbbt_commands/workflow/server
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- share/rbbt_commands/workflow/task
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- share/rbbt_commands/workflow/trace
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442
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+
- share/rbbt_commands/workflow/write_info
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- share/unicorn.rb
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- share/workflow_config.ru
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- test/rbbt/annotations/test_util.rb
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@@ -515,6 +518,7 @@ files:
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- test/rbbt/util/test_log.rb
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- test/rbbt/util/test_misc.rb
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- test/rbbt/util/test_open.rb
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521
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+
- test/rbbt/util/test_procpath.rb
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- test/rbbt/util/test_python.rb
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- test/rbbt/util/test_semaphore.rb
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- test/rbbt/util/test_simpleDSL.rb
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@@ -562,6 +566,7 @@ test_files:
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- test/rbbt/workflow/test_task.rb
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567
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- test/rbbt/resource/test_path.rb
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- test/rbbt/util/test_colorize.rb
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569
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+
- test/rbbt/util/test_procpath.rb
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- test/rbbt/util/misc/test_omics.rb
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566
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- test/rbbt/util/misc/test_pipes.rb
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567
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- test/rbbt/util/misc/test_format.rb
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