rbbt-util 5.26.87 → 5.26.88

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 658585f6a78ccc8f2a4579b1b512a9470030edbd1e724addb2b5f1ef3b71c218
-  data.tar.gz: cb64eb69d269a924b585745f6fa4be0aad88c4ed62a9510e9a85ddc3f243caf3
+  metadata.gz: 9ea3940c476d54994086edb928a7f3bd8e0f9106cf702fc5383c10dbf43df2f8
+  data.tar.gz: 842453f1c75c7d67307a9d7196273a233cc00d4a4adb27d4cb62d8c41111f748
 SHA512:
-  metadata.gz: 58458df66b0881d89894db3c526dd21b5490de6e0e55c403ef44c09827b36c3da90509d3158d8cc5438a1d3f235a6f0650eb470d0b79c3919e216879341d87aa
-  data.tar.gz: c5e2964e08101856061dd68103b2a970518d1542c163cb17d2c4f0bbe40b92a3cf225ec0859d2b97d2138d6cdf08ada9f69020555c11acafbe6bcd2bbcdb809b
+  metadata.gz: 5d679b8414ef4ed9463e2a214edf51375f417c8f6c5b5b576619efda32fd100f9d3fc623164b3e685b6bee31136a1219cf78a4d0955f5c3661c305598addeab8
+  data.tar.gz: 88e3ad03874491db2536aad2c64269fb165a92aa944101c98d59013b91eb2f05c47bf0680931f849a2a1de4422fe7bde7b7c261e915604141b8c31ee5026fbeb

data/lib/rbbt/hpc.rb

@@ -473,11 +473,21 @@ EOF
       end
     end
   end
-end
 
-if __FILE__ == $0
-  Log.severity = 0
-  iii Marenostrum::SLURM.run('ls', nil, nil, :qos => "debug", :user => 'bsc26892') if __FILE__ == $0
-end
+  def relay(job, options={})
+    options = Misc.add_defaults options, :target => 'mn1', :search_path => 'user'
+    done_deps = job.dependencies.select do |dep|
+      dep.done? 
+    end
+
+    error_deps = job.dependencies.select do |dep|
+      dep.error? && ! dep.recoverable_error?
+    end
 
+    (done_deps + error_deps).each do |dep|
+      Step.migrate(dep.path, options[:search_path], options)
+    end
+
+  end
+end
 

data/lib/rbbt/workflow/definition.rb

@@ -73,8 +73,7 @@ module Workflow
       set_info :result_type, dep.info[:result_type]
       forget = config :forget_dep_tasks, :forget_dep_tasks, :default => FORGET_DEP_TASKS
       if forget
-        self.set_info :archived_info, archived_info
-        self.set_info :archived_dependencies, info[:dependencies]
+        self.archive
         self.dependencies = self.dependencies - [dep]
         Open.rm_rf self.files_dir if Open.exist? self.files_dir
         FileUtils.cp_r dep.files_dir, self.files_dir if Open.exist? dep.files_dir

data/lib/rbbt/workflow/remote/ssh/adaptor.rb

@@ -1,20 +1,6 @@
-module WorkflowSSHClient
-  def self.__prepare_inputs_for_restclient(inputs)
-    inputs.each do |k,v|
-      if v.respond_to? :path and not v.respond_to? :original_filename
-        class << v
-          def original_filename
-            File.expand_path(path)
-          end
-        end
-      end
-
-      if Array === v and v.empty?
-        inputs[k] = "EMPTY_ARRAY"
-      end
-    end
-  end
+require 'rbbt/workflow/remote/ssh/driver'
 
+module WorkflowSSHClient
   def workflow_description
     WorkflowSSHClient.get_raw(File.join(url, 'description'))
   end
@@ -26,20 +12,20 @@ module WorkflowSSHClient
 
   def task_info(task)
     @task_info ||= IndiferentHash.setup({})
-    @task_info[task]
     
     if @task_info[task].nil?
-      task_info = WorkflowSSHClient.get_json(File.join(url, task.to_s, 'info'))
+      task_info = WorkflowSSHClient.get_json(File.join(@base_url, task.to_s))
       task_info = WorkflowSSHClient.fix_hash(task_info)
 
-      task_info[:result_type] = task_info[:result_type].to_sym
-      task_info[:export] = task_info[:export].to_sym
+      task_info[:result_type] = task_info[:result_type].to_sym if task_info[:result_type]
+      task_info[:export] = task_info[:export].to_sym if task_info[:export]
       task_info[:input_types] = WorkflowSSHClient.fix_hash(task_info[:input_types], true)
       task_info[:inputs] = task_info[:inputs].collect{|input| input.to_sym }
 
-      @task_info[task] = task_info
+      @task_info[task] = IndiferentHash.setup(task_info)
     end
-    @task_info[task]
+
+    IndiferentHash.setup(@task_info[task])
   end
 
   def tasks
@@ -72,7 +58,4 @@ module WorkflowSSHClient
     @exec_exports = @stream_exports = @synchronous_exports = []
     @asynchronous_exports = @task_info.keys
   end
-
-  def self.execute_job(base_url, task, task_params, cache_type)
-  end
 end

data/lib/rbbt/workflow/remote/ssh/driver.rb

@@ -0,0 +1,147 @@
+module SSHDriver
+  def self.run(server, script)
+    Log.debug "Run ssh script in #{server}:\n#{script}"
+    CMD.cmd("ssh '#{server}' 'shopt -s expand_aliases; bash -ic \"ruby\"' ", :in => script, :log => true).read
+  end
+
+  #def self.run_log(server, script)
+  #  Log.debug "Run and monitor ssh script in #{server}:\n#{script}"
+  #  CMD.cmd("ssh '#{server}' 'shopt -s expand_aliases; bash -ic \"ruby\"' ", :in => script, :log => true)
+  #end
+
+  def self.parse_url(url)
+    m = url.match(/ssh:\/\/([^:]+):(.*)/)
+    server = m.captures[0]
+    path = m.captures[1]
+    [server, path]
+  end
+
+  def self.path_script(path) 
+
+    workflow, task, job, *rest = path.split("/")
+    
+    script =<<-EOF
+require 'rbbt/workflow'
+wf = Workflow.require_workflow "#{workflow}"
+    EOF
+
+    case task
+    when nil
+      script +=<<-EOF
+task_info = {}
+wf.tasks.keys.each do |task|
+  task_info[task] = wf.task_info(task)
+end
+res = task_info
+      EOF
+    when 'documentation'
+      script +=<<-EOF
+res = documentation = wf.documentation
+      EOF
+    else
+      if job.nil?
+        script +=<<-EOF
+task = '#{task}'
+res = task_info = wf.task_info(task)
+        EOF
+      else
+        case rest.first
+        when nil
+          script +=<<-EOF
+task = '#{task}'
+jobname = '#{job}'
+res = job = wf.fast_load_id(File.join(task, jobname))
+          EOF
+        when "info"
+          script +=<<-EOF
+task = '#{task}'
+jobname = '#{job}'
+job = wf.fast_load_id(File.join(task, jobname))
+res = job_info = job.info
+          EOF
+        else
+          raise "Unkown path: #{[path, rest].inspect}"
+        end
+      end
+    end
+  end
+
+  def self.job_script(inputs_id, jobname = nil)
+    script =<<-EOF
+jobname = #{jobname.nil? ? 'nil' : "'#{jobname}'"}
+path = File.join(ENV["HOME"], '.rbbt/tmp/tmp-ssh_job_inputs/#{inputs_id}')
+job_inputs = Workflow.load_inputs(path, task_info[:inputs], task_info[:input_types])
+job = wf.job(task, jobname, job_inputs)
+    EOF
+    script
+  end
+
+  def self.get_json(url, params)
+    server, path = parse_url(url)
+    script = path_script(path)
+
+    script +=<<-EOF
+STDOUT.write res.to_json
+    EOF
+
+    JSON.parse(self.run(server, script))
+  end
+
+  def self.get_raw(url, params)
+    server, path = parse_url(url)
+    script = path_script(path)
+
+    script +=<<-EOF
+STDOUT.write res
+    EOF
+
+    self.run(server, script)
+  end
+
+  def self.post_job(url, inputs_id, jobname = nil)
+    server, path = parse_url(url)
+
+    script = path_script(path)
+    script += job_script(inputs_id, jobname)
+    script +=<<-EOF
+job.init_info
+STDOUT.write job.name
+    EOF
+    @name = self.run(server, script)
+  end
+
+  def self.run_job(url, input_id, jobname = nil)
+    server, path = parse_url(url)
+    
+    script = path_script(path)
+    script += job_script(input_id, jobname)
+    script +=<<-EOF
+job.produce
+STDOUT.write job.path
+    EOF
+    self.run(server, script)
+  end
+
+  def self.run_slurm_job(url, input_id, jobname = nil)
+    server, path = parse_url(url)
+    
+    script = path_script(path)
+    script += job_script(input_id, jobname)
+    script +=<<-EOF
+job.produce
+STDOUT.write job.path
+    EOF
+    self.run(server, script)
+  end
+
+  def self.clean(url, input_id, jobname = nil)
+    server, path = parse_url(url)
+    
+    script = path_script(path)
+    script +=<<-EOF
+job.clean
+    EOF
+    self.run(server, script)
+  end
+
+end

data/lib/rbbt/workflow/remote/ssh/get.rb

@@ -1,150 +1,3 @@
-module SSHClient
-  def self.run(server, script)
-    Log.debug "Run ssh script in #{server}:\n#{script}"
-    CMD.cmd("ssh '#{server}' ruby ", :in => script).read.strip
-  end
-
-  def self.run_log(server, script)
-    Log.debug "Run and monitor ssh script in #{server}:\n#{script}"
-    CMD.cmd_log("ssh '#{server}' ruby ", :in => script)
-  end
-
-  def self.parse_url(url)
-    m = url.match(/ssh:\/\/([^:]+):(.*)/)
-    server = m.captures[0]
-    path = m.captures[1]
-    [server, path]
-  end
-
-  def self.path_script(path) 
-
-    workflow, task, job, *rest = path.split("/")
-    
-    script =<<-EOF
-require 'rbbt/workflow'
-wf = Workflow.require_workflow "#{workflow}"
-    EOF
-    case task
-    when nil
-      script +=<<-EOF
-task_info = {}
-wf.tasks.keys.each do |task|
-  task_info[task] = wf.task_info(task)
-end
-res = task_info
-      EOF
-    when 'documentation'
-      script +=<<-EOF
-res = documentation = wf.documentation
-      EOF
-    else
-      if job.nil?
-        script +=<<-EOF
-task = '#{task}'
-res = task_info = wf.task_info(task)
-        EOF
-      else
-        case rest.first
-        when nil
-          script +=<<-EOF
-task = '#{task}'
-jobname = '#{job}'
-res = job = wf.fast_load_id(File.join(task, jobname))
-          EOF
-        when "info"
-          script +=<<-EOF
-task = '#{task}'
-jobname = '#{job}'
-job = wf.fast_load_id(File.join(task, jobname))
-res = job_info = job.info
-          EOF
-        else
-          raise "Unkown path: #{[path, rest].inspect}"
-        end
-      end
-    end
-  end
-
-  def self.get_json(url, params)
-    server, path = parse_url(url)
-    script = path_script(path)
-
-    script +=<<-EOF
-puts res.to_json
-    EOF
-
-    JSON.parse(self.run(server, script))
-  end
-
-  def self.get_raw(url, params)
-    server, path = parse_url(url)
-    script = path_script(path)
-
-    script +=<<-EOF
-puts res
-    EOF
-
-    self.run(server, script)
-  end
-
-  def self.post_job(url, inputs, input_types, jobname = nil)
-    server, path = parse_url(url)
-    script = path_script(path)
-    
-    id = "inputs-" << rand(100000).to_s
-    CMD.cmd("ssh '#{server}' mkdir -p .rbbt/tmp/tmp-ssh_job_inputs/ ", :in => script).read
-    TmpFile.with_file do |dir|
-      if Step.save_inputs(inputs, input_types, dir)
-        CMD.cmd("scp -r '#{dir}' .rbbt/tmp/tmp-ssh_job_inputs/#{id}")
-      end
-    end
-
-    script +=<<-EOF
-jobname = #{jobname.nil? ? 'nil' : "'#{jobname}'"}
-path = '.rbbt/tmp/tmp-ssh_job_inputs/#{id}'
-job_inputs = Workflow.load_inputs(path, task_info[:inputs], task_info[:input_types])
-job = wf.job(task, jobname, job_inputs)
-Log.severity = 10
-job.fork
-puts job.name
-    EOF
-    self.run(server, script)
-  end
-
-  def self.run_job(url, inputs, input_types, jobname = nil)
-    server, path = parse_url(url)
-    script = path_script(path)
-    
-    id = "inputs-" << rand(100000).to_s
-    CMD.cmd("ssh '#{server}' mkdir -p .rbbt/tmp/tmp-ssh_job_inputs/ ", :in => script).read
-    TmpFile.with_file do |dir|
-      if Step.save_inputs(inputs, input_types, dir)
-        CMD.cmd("scp -r '#{dir}' .rbbt/tmp/tmp-ssh_job_inputs/#{id}")
-      end
-    end
-
-    script +=<<-EOF
-jobname = #{jobname.nil? ? 'nil' : "'#{jobname}'"}
-path = '.rbbt/tmp/tmp-ssh_job_inputs/#{id}'
-job_inputs = Workflow.load_inputs(path, task_info[:inputs], task_info[:input_types])
-job = wf.job(task, jobname, job_inputs)
-job.run
-    EOF
-    self.run_log(server, script)
-  end
-
-  def self.clean(url)
-    server, path = parse_url(url)
-    script = path_script(path)
-    
-    script +=<<-EOF
-job.clean
-    EOF
-    self.run(server, script)
-  end
-
-end
-
 module WorkflowSSHClient
   def self.fix_hash(hash, fix_values = false)
     fixed = {}
@@ -223,7 +76,7 @@ module WorkflowSSHClient
 
     res = capture_exception do
       Misc.insist(2, 0.5) do
-        SSHClient.get_json(url, :params => params)
+        SSHDriver.get_json(url, :params => params)
       end
     end
 
@@ -234,22 +87,32 @@ module WorkflowSSHClient
     end
   end
 
-
-  def self.post_jobname(url, inputs, input_types)
-    SSHClient.post_job(url, inputs, input_types)
+  def self.upload_inputs(server, inputs, input_types, input_id)
+    TmpFile.with_file do |dir|
+      if Step.save_inputs(inputs, input_types, dir)
+        CMD.cmd("ssh '#{server}' mkdir -p .rbbt/tmp/tmp-ssh_job_inputs/; scp -r '#{dir}' #{server}:.rbbt/tmp/tmp-ssh_job_inputs/#{input_id}")
+      end
+    end
   end
 
+  #{{{ RUN
+  
+
   def init_job(cache_type = nil, other_params = {})
     cache_type = :asynchronous if cache_type.nil? and not @is_exec
     cache_type = :exec if cache_type.nil?
     @last_info_time = nil
     @done = false
-    get_streams
+    @server, @server_path = SSHDriver.parse_url base_url
+    @input_id ||= "inputs-" << rand(100000).to_s
+    @input_types = task_info(task)[:input_types]
+
+    WorkflowSSHClient.upload_inputs(@server, inputs, @input_types, @input_id)
+
     @name ||= Persist.memory("RemoteSteps", :workflow => self, :task => task, :jobname => @name, :inputs => inputs, :cache_type => cache_type) do
       Misc.insist do
-        #@adaptor.post_jobname(File.join(base_url, task.to_s), inputs.merge(other_params).merge(:jobname => @name||@base_name, :_cache_type => cache_type))
         input_types = {}
-        @adaptor.post_jobname(File.join(base_url, task.to_s), inputs, input_types)
+        SSHDriver.post_job(File.join(base_url, task.to_s), @input_id, @base_name)
       end
     end
     if Open.remote? @name
@@ -262,19 +125,26 @@ module WorkflowSSHClient
   end
 
   def path
-    server, path = SSHClient.parse_url(url)
-    "ssh://" + server + ":" + info[:path]
+    @server, @server_path = SSHDriver.parse_url @base_url
+    "ssh://" + @server + ":" + @remote_path
   end
 
-  def run(*args)
+  def produce(*args)
     input_types = {}
-    SSHClient.run_job(File.join(base_url, task.to_s), inputs, input_types)
+    init_job
+    @remote_path = SSHDriver.run_job(File.join(base_url, task.to_s), @input_id, @base_name)
+    while ! done?
+      sleep 1
+    end
   end
 
+  def run(*args)
+    produce(*args)
+  end
 
   def clean
     init_job
-    SSHClient.clean(@url) if done?
+    SSHDriver.clean(@url, @input_id, @base_name) if done?
     _restart
   end
 

data/lib/rbbt/workflow/step.rb

@@ -108,6 +108,11 @@ class Step
     @inputs || []
   end
 
+  def archive
+    self.set_info :archived_info, archived_info
+    self.set_info :archived_dependencies, info[:dependencies]
+  end
+
   def archived_info
     return info[:archived_info] if info[:archived_info]
 
@@ -223,7 +228,7 @@ class Step
 
   def result_type
     @result_type ||= if @task.nil?
-                       info[:result_type]
+                       info[:result_type] || :binary
                      else
                        @task.result_type || info[:result_type] || :string
                      end

data/share/rbbt_commands/migrate

@@ -39,6 +39,7 @@ test_str = options[:test] ? '-nv' : ''
 
 path, search_path, _sep, *other = ARGV
 
+search_path = 'user' if search_path.nil?
 resource = Rbbt
 
 path, real_paths = if options[:source]

data/test/rbbt/test_hpc.rb

@@ -0,0 +1,14 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '..', 'test_helper.rb')
+require 'rbbt/hpc'
+require 'rbbt/workflow'
+
+class TestHPC < Test::Unit::TestSuite
+  def test_relay
+    Log.severity = 0
+    Workflow.require_workflow "Translation"
+    job = Translation.job(:translate, nil, :genes => %w(TP53 KRAS))
+    Marenostrum.relay job
+
+  end
+end
+

data/test/rbbt/test_workflow.rb

@@ -205,21 +205,23 @@ class TestWorkflow < Test::Unit::TestCase
   def test_update_on_input_dependency_update
     Open.repository_dirs << File.join(ENV["HOME"],".rbbt/tmp/test/workflow")
     Log.severity = 0
-    send_input_dep_to_reverse_job = TestWF.job(:send_input_dep_to_reverse, nil, :name => "Miguel")
-    send_input_dep_to_reverse_job.clean
-    send_input_dep_to_reverse_job.run
-
-    input_dep_job = send_input_dep_to_reverse_job.step(:input_dep)
-    mtime_orig = Open.mtime send_input_dep_to_reverse_job.step(:reverse_input_text).path
-
-    sleep 2
-    input_dep_job.clean
-    input_dep_job.run
-    send_input_dep_to_reverse_job = TestWF.job(:send_input_dep_to_reverse, nil, :name => "Miguel")
-
-    send_input_dep_to_reverse_job.run
-    mtime_new = Open.mtime send_input_dep_to_reverse_job.step(:reverse_input_text).path
-    assert mtime_orig < mtime_new
+    Misc.with_env "RBBT_UPDATE", "true" do
+      send_input_dep_to_reverse_job = TestWF.job(:send_input_dep_to_reverse, nil, :name => "Miguel")
+      send_input_dep_to_reverse_job.clean
+      send_input_dep_to_reverse_job.run
+
+      input_dep_job = send_input_dep_to_reverse_job.step(:input_dep)
+      mtime_orig = Open.mtime send_input_dep_to_reverse_job.step(:reverse_input_text).path
+
+      sleep 2
+      input_dep_job.clean
+      input_dep_job.run
+      send_input_dep_to_reverse_job = TestWF.job(:send_input_dep_to_reverse, nil, :name => "Miguel")
+
+      send_input_dep_to_reverse_job.run
+      mtime_new = Open.mtime send_input_dep_to_reverse_job.step(:reverse_input_text).path
+      assert mtime_orig < mtime_new
+    end
   end
 
   def test_helper
@@ -252,9 +254,12 @@ class TestWorkflow < Test::Unit::TestCase
 
   def test_search
     str = "TEST"
-    job1 = TestWF.job(:repeat2, "subdir/Default", :number => 3).fork
-    job2 = TestWF.job(:repeat2, "subdir/Other", :number => 3).fork
-    job3 = TestWF.job(:repeat2, "Default", :number => 3).fork
+    TestWF.jobs(:repeat2).each do |name|
+      TestWF.load_name(:repeat2, name).clean
+    end
+    job1 = TestWF.job(:repeat2, "subdir/Default", :number => 3).clean.fork
+    job2 = TestWF.job(:repeat2, "subdir/Other", :number => 3).clean.fork
+    job3 = TestWF.job(:repeat2, "Default", :number => 3).clean.fork
 
     while not job1.done? and not job2.done? and not job3.done?
       sleep 1
@@ -379,10 +384,13 @@ class TestWorkflow < Test::Unit::TestCase
     job.run
     assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
     job = TestWF.job(:t3)
-    job.step(:t1).clean
-    Misc.with_env "RBBT_UPDATE_ALL_JOBS", "true" do
-      job = TestWF.job(:t3)
-      assert job.checks.select{|d| d.task_name.to_s == "t1" }.any?
+    sleep 1
+    Open.touch job.step(:t1).path
+    Misc.with_env "RBBT_UPDATE", "false" do
+      assert job.updated?
+    end
+    Misc.with_env "RBBT_UPDATE", "true" do
+      assert ! job.updated?
     end
   end
 

data/test/rbbt/workflow/remote/test_client.rb

@@ -0,0 +1,13 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt/workflow/remote/client'
+
+class TestRemote < Test::Unit::TestCase
+  def test_ssh
+    Log.severity = 0
+    client = WorkflowRemoteClient.new "ssh://localhost:Translation", "Translation"
+    job = client.job("translate", "SSH-TEST", :genes => ["TP53","KRAS"])
+    iii job.url
+    puts job.run
+  end
+end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.87
+  version: 5.26.88
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-11-22 00:00:00.000000000 Z
+date: 2019-11-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -328,6 +328,7 @@ files:
 - lib/rbbt/workflow/remote/rest/adaptor.rb
 - lib/rbbt/workflow/remote/rest/get.rb
 - lib/rbbt/workflow/remote/ssh/adaptor.rb
+- lib/rbbt/workflow/remote/ssh/driver.rb
 - lib/rbbt/workflow/remote/ssh/get.rb
 - lib/rbbt/workflow/schedule.rb
 - lib/rbbt/workflow/soap.rb
@@ -454,6 +455,7 @@ files:
 - test/rbbt/test_association.rb
 - test/rbbt/test_entity.rb
 - test/rbbt/test_fix_width_table.rb
+- test/rbbt/test_hpc.rb
 - test/rbbt/test_knowledge_base.rb
 - test/rbbt/test_monitor.rb
 - test/rbbt/test_packed_index.rb
@@ -507,6 +509,7 @@ files:
 - test/rbbt/util/test_simpleDSL.rb
 - test/rbbt/util/test_simpleopt.rb
 - test/rbbt/util/test_tmpfile.rb
+- test/rbbt/workflow/remote/test_client.rb
 - test/rbbt/workflow/step/test_dependencies.rb
 - test/rbbt/workflow/test_doc.rb
 - test/rbbt/workflow/test_step.rb
@@ -531,91 +534,93 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.4
+rubygems_version: 3.0.6
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/test_helper.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/test_association.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/test_entity.rb
+- test/rbbt/workflow/test_doc.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/remote/test_client.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/misc/test_omics.rb
+- test/rbbt/util/misc/test_pipes.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/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_R.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_filecache.rb
-- test/rbbt/util/test_misc.rb
+- test/rbbt/util/test_R.rb
 - test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
-- test/rbbt/util/misc/test_pipes.rb
-- test/rbbt/util/misc/test_bgzf.rb
-- test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/test_semaphore.rb
-- test/rbbt/util/simpleopt/test_get.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/test_open.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_log.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/util/R/test_plot.rb
-- test/rbbt/util/R/test_model.rb
-- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/test_python.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_parser.rb
-- test/rbbt/tsv/test_field_index.rb
-- test/rbbt/tsv/test_stream.rb
-- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_packed_index.rb
 - test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/parallel/test_through.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
-- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_parser.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_attach.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_parallel.rb
+- test/rbbt/tsv/test_manipulate.rb
 - test/rbbt/tsv/test_excel.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/test_step.rb
-- test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/test_entity.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_persist.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_leveldb.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/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_sharder.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_knowledge_base.rb
-- test/rbbt/resource/test_path.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