rbbt-util 5.32.9 → 5.32.15

data/share/rbbt_commands/hpc/orchestrate

@@ -19,16 +19,24 @@ $slurm_options = SOPT.get <<EOF
 -e--exclusive Make exclusive use of the node
 -hm--highmem Make use of highmem cores
 -wc--wipe_container* Wipe the jobs from the contain directory
+-pd--purge_deps Purge job dependencies
 -CS--contain_and_sync Contain and sync to default locations
 -ci--copy_image When using a container directory, copy image there
 -t--tail Tail the logs
 -BPP--batch_procpath* Save Procpath performance for batch job; specify only options
 -q--queue* Queue
 -t--task_cpus* Tasks
--W--workflows* Additional workflows
 -tm--time* Time
--OR--orchestration_rules* Orchestration rules
+-m--mem* SLURM minimum memory
+--gres* SLURM Generic resources
+-mcpu--mem_per_cpu* SLURM minimum memory per CPU
+-lin--licenses* SLURM licenses
+-cons--constraint* SLURM constraint
+-W--workflows* Additional workflows
 -rmb--remove_batch_basedir Remove the SLURM working directory (command, STDIN, exit status, ...)
+-lmod--lua_modules* Lua Modules to load 
+-bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
+-OR--orchestration_rules* Orchestration rules
 EOF
 
 batch_system = $slurm_options.delete :batch_system

data/share/rbbt_commands/hpc/task

@@ -18,15 +18,22 @@ $slurm_options = SOPT.get <<EOF
 -e--exclusive Make exclusive use of the node
 -hm--highmem Make use of highmem cores
 -wc--wipe_container* Wipe the jobs from the contain directory
+-pd--purge_deps Purge job dependencies
 -CS--contain_and_sync Contain and sync to default locations
 -ci--copy_image When using a container directory, copy image there
 -t--tail Tail the logs
 -BPP--batch_procpath* Save Procpath performance for batch job; specify only options
 -q--queue* Queue
 -t--task_cpus* Tasks
--W--workflows* Additional workflows
 -tm--time* Time
+-m--mem* SLURM minimum memory
+--gres* SLURM Generic resources
+-mcpu--mem_per_cpu* SLURM minimum memory per CPU
+-lin--licenses* SLURM licenses
+-cons--constraint* SLURM constraint
+-W--workflows* Additional workflows
 -rmb--remove_batch_dir Remove the batch working directory (command, STDIN, exit status, ...)
+-lmod--lua_modules* Lua Modules to load 
 -bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
 EOF
 

data/share/rbbt_commands/lsf/list

@@ -173,7 +173,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    select = true if queued && deps && (running_jobs & deps).any? || queued && is_running && nodes.empty?
    select = true if running && nodes.any? && (exit_status.nil? && running_jobs.include?(id)) && (!deps || (running_jobs & deps).empty?)
    select = true if jobid && jobid.split(",").include?(id)
-   select = select && cmd.match(/#{search}/) if search
+   select = select && step_path.match(/#{search}/) if search
    next unless select 
  elsif search
    select = false
@@ -206,9 +206,9 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    puts Log.color(:magenta, "BATCH parameters: ")
    case job_batch_system 
    when 'slurm'
-     text = CMD.cmd('grep "^#SBATCH" |tail -n +5', :in => Open.read(fcmd)).read.strip
+     text = CMD.cmd('grep "^#SBATCH" ', :in => Open.read(fcmd)).read.strip
    when 'lsf'
-     text = CMD.cmd('grep "^#BSUB" |tail -n +5', :in => Open.read(fcmd)).read.strip
+     text = CMD.cmd('grep "^#BSUB" ', :in => Open.read(fcmd)).read.strip
    else
      text = ""
    end
@@ -292,13 +292,17 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
      step_path = step_line.split(": ").last.strip
      step = Step.new step_path
      step.load_dependencies_from_info
+     has_bar = false
      (step.rec_dependencies + [step]).reverse.each do |j|
        next if j.done? 
-       next unless j.file(:progress).exists?
-       bar = Log::ProgressBar.new 
-       bar.load(j.file(:progress).yaml)
-       puts Log.color(:magenta, "Progress: ") + bar.report_msg + " " + Log.color(:yellow, j.task_signature)
+       if j.file(:progress).exists?
+         bar = Log::ProgressBar.new 
+         bar.load(j.file(:progress).yaml)
+         puts Log.color(:magenta, "Progress: ") + bar.report_msg + " " + Log.color(:yellow, j.task_signature)
+         has_bar = true
+       end
      end
+     puts Log.color(:magenta, "Progress: ") + Log.color(:yellow, step.task_signature) + " #{step.status}" unless has_bar
    end
  end
 

data/share/rbbt_commands/lsf/orchestrate

@@ -19,16 +19,24 @@ $slurm_options = SOPT.get <<EOF
 -e--exclusive Make exclusive use of the node
 -hm--highmem Make use of highmem cores
 -wc--wipe_container* Wipe the jobs from the contain directory
+-pd--purge_deps Purge job dependencies
 -CS--contain_and_sync Contain and sync to default locations
 -ci--copy_image When using a container directory, copy image there
 -t--tail Tail the logs
 -BPP--batch_procpath* Save Procpath performance for batch job; specify only options
 -q--queue* Queue
 -t--task_cpus* Tasks
--W--workflows* Additional workflows
 -tm--time* Time
--OR--orchestration_rules* Orchestration rules
+-m--mem* SLURM minimum memory
+--gres* SLURM Generic resources
+-mcpu--mem_per_cpu* SLURM minimum memory per CPU
+-lin--licenses* SLURM licenses
+-cons--constraint* SLURM constraint
+-W--workflows* Additional workflows
 -rmb--remove_batch_basedir Remove the SLURM working directory (command, STDIN, exit status, ...)
+-lmod--lua_modules* Lua Modules to load 
+-bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
+-OR--orchestration_rules* Orchestration rules
 EOF
 
 batch_system = $slurm_options.delete :batch_system

data/share/rbbt_commands/lsf/task

@@ -18,15 +18,22 @@ $slurm_options = SOPT.get <<EOF
 -e--exclusive Make exclusive use of the node
 -hm--highmem Make use of highmem cores
 -wc--wipe_container* Wipe the jobs from the contain directory
+-pd--purge_deps Purge job dependencies
 -CS--contain_and_sync Contain and sync to default locations
 -ci--copy_image When using a container directory, copy image there
 -t--tail Tail the logs
 -BPP--batch_procpath* Save Procpath performance for batch job; specify only options
 -q--queue* Queue
 -t--task_cpus* Tasks
--W--workflows* Additional workflows
 -tm--time* Time
+-m--mem* SLURM minimum memory
+--gres* SLURM Generic resources
+-mcpu--mem_per_cpu* SLURM minimum memory per CPU
+-lin--licenses* SLURM licenses
+-cons--constraint* SLURM constraint
+-W--workflows* Additional workflows
 -rmb--remove_batch_dir Remove the batch working directory (command, STDIN, exit status, ...)
+-lmod--lua_modules* Lua Modules to load 
 -bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
 EOF
 

data/share/rbbt_commands/slurm/list

@@ -173,7 +173,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    select = true if queued && deps && (running_jobs & deps).any? || queued && is_running && nodes.empty?
    select = true if running && nodes.any? && (exit_status.nil? && running_jobs.include?(id)) && (!deps || (running_jobs & deps).empty?)
    select = true if jobid && jobid.split(",").include?(id)
-   select = select && cmd.match(/#{search}/) if search
+   select = select && step_path.match(/#{search}/) if search
    next unless select 
  elsif search
    select = false
@@ -206,9 +206,9 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    puts Log.color(:magenta, "BATCH parameters: ")
    case job_batch_system 
    when 'slurm'
-     text = CMD.cmd('grep "^#SBATCH" |tail -n +5', :in => Open.read(fcmd)).read.strip
+     text = CMD.cmd('grep "^#SBATCH" ', :in => Open.read(fcmd)).read.strip
    when 'lsf'
-     text = CMD.cmd('grep "^#BSUB" |tail -n +5', :in => Open.read(fcmd)).read.strip
+     text = CMD.cmd('grep "^#BSUB" ', :in => Open.read(fcmd)).read.strip
    else
      text = ""
    end
@@ -292,13 +292,17 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
      step_path = step_line.split(": ").last.strip
      step = Step.new step_path
      step.load_dependencies_from_info
+     has_bar = false
      (step.rec_dependencies + [step]).reverse.each do |j|
        next if j.done? 
-       next unless j.file(:progress).exists?
-       bar = Log::ProgressBar.new 
-       bar.load(j.file(:progress).yaml)
-       puts Log.color(:magenta, "Progress: ") + bar.report_msg + " " + Log.color(:yellow, j.task_signature)
+       if j.file(:progress).exists?
+         bar = Log::ProgressBar.new 
+         bar.load(j.file(:progress).yaml)
+         puts Log.color(:magenta, "Progress: ") + bar.report_msg + " " + Log.color(:yellow, j.task_signature)
+         has_bar = true
+       end
      end
+     puts Log.color(:magenta, "Progress: ") + Log.color(:yellow, step.task_signature) + " #{step.status}" unless has_bar
    end
  end
 

data/share/rbbt_commands/slurm/orchestrate

@@ -19,16 +19,24 @@ $slurm_options = SOPT.get <<EOF
 -e--exclusive Make exclusive use of the node
 -hm--highmem Make use of highmem cores
 -wc--wipe_container* Wipe the jobs from the contain directory
+-pd--purge_deps Purge job dependencies
 -CS--contain_and_sync Contain and sync to default locations
 -ci--copy_image When using a container directory, copy image there
 -t--tail Tail the logs
 -BPP--batch_procpath* Save Procpath performance for batch job; specify only options
 -q--queue* Queue
 -t--task_cpus* Tasks
--W--workflows* Additional workflows
 -tm--time* Time
--OR--orchestration_rules* Orchestration rules
+-m--mem* SLURM minimum memory
+--gres* SLURM Generic resources
+-mcpu--mem_per_cpu* SLURM minimum memory per CPU
+-lin--licenses* SLURM licenses
+-cons--constraint* SLURM constraint
+-W--workflows* Additional workflows
 -rmb--remove_batch_basedir Remove the SLURM working directory (command, STDIN, exit status, ...)
+-lmod--lua_modules* Lua Modules to load 
+-bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
+-OR--orchestration_rules* Orchestration rules
 EOF
 
 batch_system = $slurm_options.delete :batch_system

data/share/rbbt_commands/slurm/task

@@ -18,15 +18,22 @@ $slurm_options = SOPT.get <<EOF
 -e--exclusive Make exclusive use of the node
 -hm--highmem Make use of highmem cores
 -wc--wipe_container* Wipe the jobs from the contain directory
+-pd--purge_deps Purge job dependencies
 -CS--contain_and_sync Contain and sync to default locations
 -ci--copy_image When using a container directory, copy image there
 -t--tail Tail the logs
 -BPP--batch_procpath* Save Procpath performance for batch job; specify only options
 -q--queue* Queue
 -t--task_cpus* Tasks
--W--workflows* Additional workflows
 -tm--time* Time
+-m--mem* SLURM minimum memory
+--gres* SLURM Generic resources
+-mcpu--mem_per_cpu* SLURM minimum memory per CPU
+-lin--licenses* SLURM licenses
+-cons--constraint* SLURM constraint
+-W--workflows* Additional workflows
 -rmb--remove_batch_dir Remove the batch working directory (command, STDIN, exit status, ...)
+-lmod--lua_modules* Lua Modules to load 
 -bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
 EOF
 

data/share/rbbt_commands/workflow/forget_deps

@@ -38,11 +38,11 @@ step.copy_files_dir
 dependencies = step.dependencies
 
 if remove && remove.any?
- remove_paths = dependencies.select do |dep|
-  remove.include?(dep.task_name) || remove.include?([dep.workflow.to_s, dep.task_name] * "#")
- end.collect{|dep| dep.path } 
+  remove_paths = dependencies.select do |dep|
+    remove.include?(dep.task_name) || remove.include?([dep.workflow.to_s, dep.task_name] * "#")
+  end.collect{|dep| dep.path } 
 else
- remove_paths = dependencies.collect{|dep| dep.path }
+  remove_paths = dependencies.collect{|dep| dep.path }
 end
 
 step.set_info :dependencies, step.info[:dependencies].reject{|info| remove_paths.include? info.last}
@@ -50,6 +50,7 @@ step.set_info :dependencies, step.info[:dependencies].reject{|info| remove_paths
 if options[:purge] || options[:recursive_purge]
   dependencies.each do |dependency|
     next unless remove_paths.include? dependency.path
+    next unless Open.exists?(dependency.info_file)
     Step.purge(dependency.path, options[:recursive_purge])
   end
 end

data/test/rbbt/util/test_python.rb

@@ -2,6 +2,7 @@ require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helpe
 require 'rbbt/util/python'
 
 class TestPython < Test::Unit::TestCase
+
   def test_python
     TmpFile.with_file do |tmpdir|
       code =<<-EOF
@@ -67,7 +68,7 @@ def python_print():
 
   def test_keras
     defined = RbbtPython.run do
-      pyimport "keras.models", as: :km
+      pyimport "tensorflow.keras.models", as: :km
       defined?(km.Sequential)
     end
     assert defined
@@ -75,7 +76,7 @@ def python_print():
 
   def test_keras_import
     defined = RbbtPython.run do
-      pyfrom "keras.models", import: :Sequential
+      pyfrom "tensorflow.keras.models", import: :Sequential
       defined?(self::Sequential)
     end
     assert defined

data/test/rbbt/util/test_simpleDSL.rb

@@ -35,12 +35,12 @@ class TestDSL < Test::Unit::TestCase
 
   def test_config
     config = <<-EOC
-  action1("Hello")
-  action2("Good bye")
+  action1 "Hello"  
+  action2 "Good bye" 
     EOC
 
     begin
-      assert(@parser.config(:action) == config)
+      assert_equal config.split("\n").collect{|l| l.strip}, @parser.config(:action).split("\n").collect{|l| l.strip}
     rescue SimpleDSL::NoRuby2Ruby
     end
   end

data/test/rbbt/workflow/util/test_data.rb

@@ -0,0 +1,48 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt/workflow/util/data'
+
+module TestDataWF
+  extend Workflow
+  extend Workflow::Data
+
+  input :salutation, :string
+  task :salute_luis => :string do |name,salutation|
+    "Hi Luis: #{salutation}"
+  end
+
+  input :name, :string
+  input :salutation, :string
+  task :salute => :string do |name,salutation|
+    "Hi #{name}: #{salutation}"
+  end
+
+  data_task :salute_data, TestDataWF, :salute, :salutation => :placeholder do |directory,options|
+    options.merge({:salutation => directory.salutation.read})
+  end
+
+  data_task :salute_data2, TestDataWF, :salute, :salutation => :placeholder do |directory,options|
+    {:task => :salute_luis, :inputs => options.merge({:salutation => directory.salutation.read})}
+  end
+end
+
+class TestWorkflowData < Test::Unit::TestCase
+  def test_workflow_data
+    TmpFile.with_file do |tmpdir|
+      tmpdir = Path.setup(tmpdir.dup)
+
+      Open.write(tmpdir.TestDir.options.name, "Miguel")
+      Open.write(tmpdir.TestDir.salutation, "My salutations")
+
+      TestDataWF.data tmpdir
+
+      job = TestDataWF.job(:salute_data, "TestDir")
+      job.recursive_clean.run
+      assert job.run.include? "Miguel"
+
+      job = TestDataWF.job(:salute_data2, "TestDir")
+      job.recursive_clean.run
+      assert job.run.include? "Luis"
+    end
+  end
+end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.32.9
+  version: 5.32.15
 platform: ruby
 authors:
 - Miguel Vazquez
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-05-03 00:00:00.000000000 Z
+date: 2021-06-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -344,9 +344,11 @@ files:
 - lib/rbbt/workflow/task.rb
 - lib/rbbt/workflow/usage.rb
 - lib/rbbt/workflow/util/archive.rb
+- lib/rbbt/workflow/util/data.rb
 - lib/rbbt/workflow/util/orchestrator.rb
 - lib/rbbt/workflow/util/provenance.rb
 - lib/rbbt/workflow/util/trace.rb
+- python/rbbt.py
 - share/Rlib/plot.R
 - share/Rlib/svg.R
 - share/Rlib/util.R
@@ -549,13 +551,14 @@ files:
 - test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_task.rb
 - test/rbbt/workflow/util/test_archive.rb
+- test/rbbt/workflow/util/test_data.rb
 - test/rbbt/workflow/util/test_orchestrator.rb
 - test/test_helper.rb
 homepage: http://github.com/mikisvaz/rbbt-util
 licenses:
 - MIT
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -570,104 +573,104 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project:
-rubygems_version: 2.7.6
-signing_key:
+rubygems_version: 3.1.4
+signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/test_helper.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_association.rb
-- test/rbbt/hpc/test_slurm.rb
-- test/rbbt/hpc/test_batch.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/test_packed_index.rb
 - test/rbbt/test_entity.rb
-- test/rbbt/test_fix_width_table.rb
 - test/rbbt/workflow/test_remote_workflow.rb
-- test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/test_schedule.rb
 - test/rbbt/workflow/util/test_archive.rb
 - test/rbbt/workflow/util/test_orchestrator.rb
-- test/rbbt/workflow/test_task.rb
+- test/rbbt/workflow/util/test_data.rb
+- test/rbbt/workflow/test_doc.rb
+- test/rbbt/workflow/test_schedule.rb
 - test/rbbt/workflow/test_step.rb
-- test/rbbt/test_tsv.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/util/test_migrate.rb
-- test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_semaphore.rb
-- test/rbbt/util/test_procpath.rb
-- test/rbbt/util/R/test_model.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/util/R/test_plot.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_concurrency.rb
+- test/rbbt/workflow/step/test_dependencies.rb
+- test/rbbt/workflow/test_task.rb
+- test/rbbt/resource/test_path.rb
 - test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_config.rb
-- test/rbbt/util/test_log.rb
-- test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/test_python.rb
-- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_procpath.rb
+- test/rbbt/util/misc/test_development.rb
 - test/rbbt/util/misc/test_omics.rb
+- test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/misc/test_format.rb
 - test/rbbt/util/misc/test_lock.rb
 - test/rbbt/util/misc/test_multipart_payload.rb
 - test/rbbt/util/misc/test_bgzf.rb
-- test/rbbt/util/misc/test_development.rb
-- test/rbbt/util/misc/test_format.rb
-- test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/test_concurrency.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/R/test_plot.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/test_config.rb
+- test/rbbt/util/test_log.rb
+- test/rbbt/util/test_simpleDSL.rb
 - test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_R.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/resource/test_path.rb
-- test/rbbt/test_hpc.rb
-- test/rbbt/test_persist.rb
+- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_misc.rb
+- test/rbbt/util/test_open.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/test_python.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- test/rbbt/util/test_semaphore.rb
+- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_migrate.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_packed_index.rb
+- test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_filter.rb
 - test/rbbt/tsv/test_parser.rb
 - test/rbbt/tsv/test_csv.rb
-- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_matrix.rb
 - test/rbbt/tsv/test_field_index.rb
 - test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_stream.rb
+- test/rbbt/tsv/test_index.rb
 - test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_matrix.rb
-- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_manipulate.rb
 - test/rbbt/tsv/test_excel.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
 - test/rbbt/tsv/parallel/test_through.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/test_stream.rb
+- test/rbbt/test_association.rb
+- test/rbbt/hpc/test_batch.rb
+- test/rbbt/hpc/test_slurm.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_lmdb.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
+- test/rbbt/persist/test_tsv.rb
+- test/rbbt/test_tsv.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/test_fix_width_table.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/test_hpc.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/test_persist.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/test_helper.rb