rbbt-util 5.20.21 → 5.20.22

data/bin/rbbt

@@ -4,6 +4,7 @@ dev_dir = nil
 if _i = ARGV.index("--dev")
   dev_dir = ARGV[_i+1]
   ARGV.delete "--dev"
+  ARGV.delete dev_dir
 end
 
 if dev_dir.nil? 

data/lib/rbbt/rest/client/step.rb

@@ -88,6 +88,10 @@ class WorkflowRESTClient
       (Array === @url ? @url.first : @url).split("/").last
     end
 
+    def name=(name)
+      @url = [base_url,task, name] * "/"
+    end
+
     def task_name
       return task if task
       init_job

data/lib/rbbt/tsv/parser.rb

@@ -1,7 +1,7 @@
 require 'rbbt/util/cmd'
 module TSV
   class Parser
-    attr_accessor :stream, :filename, :header_hash, :sep, :sep2, :type, :key_position, :field_positions, :cast, :key_field, :fields, :fix, :select, :serializer, :straight, :take_all, :zipped, :namespace, :first_line, :stream, :preamble, :identifiers
+    attr_accessor :stream, :filename, :header_hash, :sep, :sep2, :type, :key_position, :field_positions, :cast, :key_field, :fields, :fix, :select, :serializer, :straight, :take_all, :zipped, :namespace, :first_line, :stream, :preamble, :identifiers, :header_options
 
     class SKIP_LINE < Exception; end
     class END_PARSING < Exception; end
@@ -146,8 +146,12 @@ module TSV
         raise $!
       end
 
-      str = parts[key_position]
-      keys = str.split(@sep2, -1)
+      if key_position and key_position != 0 and @header_options[:type] == :flat
+        keys = parts[1..-1]
+      else
+        str = parts[key_position]
+        keys = str.split(@sep2, -1)
+      end
 
       if @take_all
         values = parts.collect{|e| e.split(@sep2, -1) }.flatten
@@ -391,9 +395,9 @@ module TSV
       @stream = stream
 
 
-      header_options = parse_header(stream)
+      @header_options = parse_header(stream)
 
-      options = header_options.merge options
+      options = @header_options.merge options
 
       @type ||= Misc.process_options(options, :type) || :double
       @type ||= :double
@@ -435,7 +439,7 @@ module TSV
           self.instance_eval do alias add_to_data add_to_data_no_merge_double end
         end
       when :single
-        if header_options[:type] == :flat
+        if @header_options[:type] == :flat
           self.instance_eval do alias get_values get_values_single_from_flat end
           self.instance_eval do alias cast_values cast_values_single end
           self.instance_eval do alias add_to_data add_to_data_no_merge_double end
@@ -448,6 +452,7 @@ module TSV
         self.instance_eval do alias get_values get_values_list end
         self.instance_eval do alias cast_values cast_values_list end
         self.instance_eval do alias add_to_data add_to_data_no_merge_list end
+
       when :flat
         @take_all = true if field_positions.nil?
         self.instance_eval do alias cast_values cast_values_flat end
@@ -460,11 +465,11 @@ module TSV
             self.instance_eval do alias add_to_data add_to_data_flat_merge_double end
           end
         else
-          self.instance_eval do alias get_values get_values_flat end
+          self.instance_eval do alias get_values get_values_flat_merge end
           if key_position and key_position != 0 and field_positions.nil?
-            self.instance_eval do alias add_to_data add_to_data_flat_keys end
+            self.instance_eval do alias add_to_data add_to_data_flat_merge_keys end
           else
-            self.instance_eval do alias add_to_data add_to_data_flat end
+            self.instance_eval do alias add_to_data add_to_data_flat_merge_double end
           end
         end
       else

data/lib/rbbt/util/tmpfile.rb

@@ -2,12 +2,12 @@ require 'fileutils'
 
 module TmpFile
 
-  TMPDIR = "/tmp/tmpfiles" 
-  FileUtils.mkdir TMPDIR unless File.exist? TMPDIR
+  TMPDIR = "/tmp/#{ENV['USER']}/tmpfiles" 
+  FileUtils.mkdir_p TMPDIR unless File.exist? TMPDIR
 
   def self.tmpdir=(tmpdir)
     TMPDIR.replace tmpdir
-    FileUtils.mkdir TMPDIR unless File.exist? TMPDIR
+    FileUtils.mkdir_p TMPDIR unless File.exist? TMPDIR
   end
 
   def self.tmpdir

data/lib/rbbt/workflow.rb

@@ -183,10 +183,10 @@ module Workflow
   attr_accessor :task_dependencies, :task_description, :last_task 
   attr_accessor :asynchronous_exports, :synchronous_exports, :exec_exports
   attr_accessor :step_cache
+  attr_accessor :remote_tasks
 
   #{{{ ATTR DEFAULTS
   
-  
   def self.workdir=(path)
     path = Path.setup path.dup unless Path === path
     @@workdir = path
@@ -301,6 +301,8 @@ module Workflow
 
   def job(taskname, jobname = nil, inputs = {})
     taskname = taskname.to_sym
+    return remote_tasks[taskname].job(taskname, jobname, inputs) if remote_tasks and remote_tasks.include? taskname
+
     jobname = DEFAULT_NAME if jobname.nil? or jobname.empty?
 
     task = tasks[taskname]
@@ -347,10 +349,12 @@ module Workflow
   def load_id(id)
     path = File.join(workdir, id)
     task = task_for path
+    return remote_tasks[task].load_id(id) if remote_tasks and remote_tasks.include? task
     step = Step.new path, tasks[task.to_sym]
     step.info
     if step.info.include? :dependencies
       step.dependencies = step.info[:dependencies].collect do |task, job|
+        next if job.nil?
         load_id(File.join(task.to_s, job))
       end
     end
@@ -358,6 +362,7 @@ module Workflow
   end
 
   def load_name(task, name)
+    return remote_tasks[task].load_step(path) if remote_tasks and remote_tasks.include? task
     task = tasks[task.to_sym] if String === task or Symbol === task
     path = step_path task.name, name, [], [], task.extension
     get_job_step path, task

data/lib/rbbt/workflow/accessor.rb

@@ -770,4 +770,8 @@ module Workflow
     Misc.path_relative_to(workdir_find, dir).sub(/([^\/]+)\/.*/,'\1')
   end
 
+  def task_exports
+    [exec_exports, synchronous_exports, asynchronous_exports].compact.flatten.uniq
+  end
+
 end

data/lib/rbbt/workflow/step/run.rb

@@ -195,6 +195,8 @@ class Step
             FileUtils.rm pid_file if File.exist?(pid_file)
           end
 
+          set_info :dependencies, dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]}
+
           result
         end
 

data/share/rbbt_commands/workflow/server

@@ -19,9 +19,10 @@ $ rbbt workflow server [options] <Workflow>
 -f--finder Start server with finder functionality
 -R--Rserve_session* Rserve session to use, otherwise start new one
 -wd--workdir* Change the working directory of the workflow
--w--workflows* List of additional workflows to load
+-W--workflows* List of additional workflows to load
 --views* Directory with view templates
 --stream Activate streaming of workflow tasks
+--export* Export workflow tasks 
 --options* Additional options for server (e.g. option1=value1;option2=value2)
 EOF
 
@@ -52,10 +53,13 @@ ENV["RServe-session"] = options[:RServe_session] || workflow
 
 server = options[:server] || 'puma'
 
+exports = options[:export].split(/\s*,/) if options[:export]
+
 TmpFile.with_file do |app_dir|
   Misc.in_dir(app_dir) do
     app_dir = Path.setup(app_dir.dup)
     Open.write(app_dir.etc.target_workflow.find, workflow)
+    Open.write(app_dir.etc.target_workflow_exports.find, exports * "\n") if exports
     Open.write(app_dir.etc.workflows.find, workflows.split(/,\s/)*"\n") if workflows 
 
     require 'rack'

data/share/workflow_config.ru

@@ -23,12 +23,20 @@ def app_eval(app, file)
 end
 
 #{{{ INIT
-load_file Rbbt.etc['app.d/init.rb'].find
+ENV["RBBT_LOG"] = Log.severity.to_s
+require Rbbt.etc['app.d/init.rb'].find
 
 #{{{ Workflow
 workflow = Rbbt.etc['target_workflow'].read
 wf = Workflow.require_workflow workflow, true
 
+if Rbbt.etc['target_workflow_exports'].exists?
+  exports = Rbbt.etc['target_workflow_exports'].read.split("\n")
+  exports.each do |task|
+    wf.export task.to_sym
+  end
+end
+
 $title = wf.to_s
 $class_name = class_name = wf.to_s + "REST"
 $app = app = eval "class #{class_name} < Sinatra::Base; self end"

data/test/rbbt/test_tsv.rb

@@ -315,10 +315,11 @@ b 2
 a 1
 b 2
 b 3
+d 22
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :key_field => "Value", :tsv_grep => "2")
+      tsv = TSV.open(filename, :key_field => "Value", :grep => "2")
       assert(tsv.include?("2"))
       assert(! tsv.include?("3"))
     end
@@ -350,7 +351,6 @@ b 2
 
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(filename, :key_field => "Value", :grep => "#\\|2")
-      assert(! tsv.include?("1"))
       assert(tsv.include?("2"))
       assert(! tsv.include?("7"))
     end
@@ -525,6 +525,7 @@ row2    A    B    Id3
 
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(filename, :sep => /\s+/, :type => :flat, :key_field => "ValueA", :fields => ["OtherID"], :merge => true)
+      ppp tsv
       assert tsv["aaa"].include? "Id1"
       assert tsv["aaa"].include? "Id2"
  
@@ -572,4 +573,31 @@ row3    AA    BB|BBB    Id3|Id2
  
     end
   end
+
+  def test_flat_key_field_double
+    content =<<-EOF
+#Id    ValueA 
+row1   a|aa|aaa
+row2   b|bbb|bbbb|bb
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/, :key_field => "ValueA", :fields => ["Id"], :type => :flat)
+      assert tsv.include? 'aa'
+    end
+  end
+
+  def test_flat_key_field
+    content =<<-EOF
+#: :type=:flat
+#Id    ValueA 
+row1   a   aa   aaa
+row2   b  bbb bbbb bb
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/, :key_field => "ValueA", :fields => ["Id"], :type => :flat)
+      assert tsv.include? 'aa'
+    end
+  end
 end

data/test/rbbt/util/test_open.rb

@@ -148,6 +148,6 @@ class TestOpen < Test::Unit::TestCase
       assert_equal obj, obj_cp
     end
   end
-  
+
 end
 

data/test/test_helper.rb

@@ -1,3 +1,6 @@
+gem "test-unit", "~> 3.0"
+gem "minitest", "~> 5.5"
+
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 

metadata

@@ -1,153 +1,174 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.20.21
+  version: 5.20.22
+  prerelease: 
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-06-24 00:00:00.000000000 Z
+date: 2016-07-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: progress-monitor
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: lockfile
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: spreadsheet
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: highline
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: bio-bgzf
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: term-ansicolor
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rest-client
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: to_regexp
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: nakayoshi_fork
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 description: Utilities for handling tsv files, caches, etc
@@ -164,12 +185,6 @@ extra_rdoc_files:
 - README.rdoc
 files:
 - LICENSE
-- README.rdoc
-- bin/rbbt
-- bin/rbbt_Rutil.rb
-- bin/rbbt_dangling_locks.rb
-- bin/rbbt_exec.rb
-- bin/rbbt_query.rb
 - etc/app.d/base.rb
 - etc/app.d/entities.rb
 - etc/app.d/finder.rb
@@ -377,186 +392,193 @@ files:
 - share/rbbt_commands/workflow/task
 - share/unicorn.rb
 - share/workflow_config.ru
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/association/test_index.rb
+- README.rdoc
+- test/test_helper.rb
+- test/rbbt/resource/test_path.rb
 - test/rbbt/association/test_item.rb
+- test/rbbt/association/test_database.rb
 - test/rbbt/association/test_open.rb
+- test/rbbt/association/test_index.rb
 - test/rbbt/association/test_util.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/resource/test_path.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/test_association.rb
-- test/rbbt/test_entity.rb
-- test/rbbt/test_fix_width_table.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/test_persist.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_tsv.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/tsv/parallel/test_through.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_attach.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_field_index.rb
-- test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/test_matrix.rb
-- test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_parser.rb
-- test/rbbt/tsv/test_stream.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/test_concurrency.rb
+- test/rbbt/util/test_log.rb
+- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_semaphore.rb
+- test/rbbt/util/concurrency/test_threads.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_tmpfile.rb
+- test/rbbt/util/test_open.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/test_simpleDSL.rb
 - test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/misc/test_bgzf.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_R.rb
 - test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
-- test/rbbt/util/misc/test_omics.rb
 - test/rbbt/util/misc/test_pipes.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_R.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_concurrency.rb
+- test/rbbt/util/misc/test_bgzf.rb
+- test/rbbt/util/misc/test_omics.rb
+- test/rbbt/util/misc/test_multipart_payload.rb
 - test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/test_log.rb
 - test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_semaphore.rb
-- test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/test_tmpfile.rb
+- test/rbbt/test_entity.rb
 - test/rbbt/workflow/step/test_dependencies.rb
 - test/rbbt/workflow/test_doc.rb
 - test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_task.rb
-- test/test_helper.rb
+- test/rbbt/test_association.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/parallel/test_through.rb
+- test/rbbt/tsv/test_parallel.rb
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_stream.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_field_index.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/tsv/test_parser.rb
+- test/rbbt/test_packed_index.rb
+- test/rbbt/test_persist.rb
+- test/rbbt/test_fix_width_table.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_lmdb.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/persist/test_tsv.rb
+- test/rbbt/test_tsv.rb
+- bin/rbbt_query.rb
+- bin/rbbt_exec.rb
+- bin/rbbt_Rutil.rb
+- bin/rbbt
+- bin/rbbt_dangling_locks.rb
 homepage: http://github.com/mikisvaz/rbbt-util
 licenses:
 - MIT
-metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.6
+rubygems_version: 1.8.23
 signing_key: 
-specification_version: 4
+specification_version: 3
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/rbbt/test_workflow.rb
+- test/test_helper.rb
 - test/rbbt/resource/test_path.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/util/test_concurrency.rb
 - test/rbbt/util/test_log.rb
+- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_semaphore.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_open.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_R.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_pipes.rb
+- test/rbbt/util/misc/test_bgzf.rb
 - test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/misc/test_multipart_payload.rb
 - test/rbbt/util/test_excel2tsv.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_misc.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/R/test_model.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/test_association.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/test_resource.rb
 - test/rbbt/test_entity.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/test_tsv.rb
 - test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_doc.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_persist.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/persist/tsv/test_lmdb.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_tokyocabinet.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/tsv/test_field_index.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_task.rb
+- test/rbbt/test_association.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/parallel/test_through.rb
 - test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_accessor.rb
 - test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_parser.rb
 - test/rbbt/tsv/test_stream.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_accessor.rb
 - test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_matrix.rb
 - test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/parallel/test_through.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/test_field_index.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/tsv/test_parser.rb
+- test/rbbt/test_packed_index.rb
+- test/rbbt/test_persist.rb
 - test/rbbt/test_fix_width_table.rb
-- test/test_helper.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_lmdb.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/persist/test_tsv.rb
+- test/rbbt/test_tsv.rb

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