rbbt-util 5.31.15 → 5.32.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 9616d2b1893ed3444d432e99b4ef6ddaf7d61836ee1c23dbd4deb1efa767b80d
-  data.tar.gz: c5dc433a171c909eb2711ee37832fb094d271fcf6099f0394706af3cd8da1520
+  metadata.gz: 421178e8bb0a2b8631af02c890c177132a9bfdad08d62cc7bb728cab9679f8f0
+  data.tar.gz: 893045f7ff08c8bfbd1701dd6da74aee5e8b59a1f2af7d8fba21c06535f06e92
 SHA512:
-  metadata.gz: efe3b9c85ec947f900283ca4b2a3e651617558bfd7d85dbea80180ad377e18150df8fccde9efecdd2493d9e4f0ed7979dbdefe2f815e2480d910d5e507670422
-  data.tar.gz: 24bc0e0e6dda34cbf7ad4ea08cb1cbeb18b3bb55b42a79a4590183fd86e7247d7aeb648c31673ef5601f632828d71ae29594e3c6b8f5c7c860dab6592a373f68
+  metadata.gz: fd00a95c8217671959abcddd6591243afdc9920f46bbda881161eb7f60e0c08a591194057c25d8e69f1ffcd192abcea1feacfc714c032033debdfa7378e60290
+  data.tar.gz: 645deeb97dfd4b30a0e552efa5f7fede9edbb0d6936d0c3849e4354ceafcdbba41739efbd1a421e80c5fcf462a426d3765e05f04933748765ed066fb1edd168f

data/lib/rbbt/hpc/lsf.rb

@@ -7,10 +7,13 @@ module HPC
 
     def self.batch_system_variables
       <<-EOF
-[[ -z $LSB_MAX_MEM_RUSAGE ]] || MAX_MEMORY=$LSB_MAX_MEM_RUSAGE 
-[[ -z $MAX_MEMORY ]] && let MAX_MEMORY="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / 1024"
-BATCH_JOB_ID=$LSF_JOBID
-BATCH_SYSTEM=LSF
+let TOTAL_PROCESORS="$(cat /proc/cpuinfo|grep ^processor |wc -l)"
+let MAX_MEMORY_DEFAULT="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / ( (1024 * $TOTAL_PROCESORS) / $LSB_MAX_NUM_PROCESSORS )"
+[ ! -z $LSB_MAX_MEM_RUSAGE ] && let MAX_MEMORY="$LSB_MAX_MEM_RUSAGE" || MAX_MEMORY="$MAX_MEMORY_DEFAULT"
+export MAX_MEMORY_DEFAULT
+export MAX_MEMORY
+export BATCH_JOB_ID=$LSF_JOBID
+export BATCH_SYSTEM=LSF
       EOF
     end
 

data/lib/rbbt/hpc/slurm.rb

@@ -8,7 +8,8 @@ module HPC
 
     def self.batch_system_variables
       <<-EOF
-let MAX_MEMORY_DEFAULT="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / ( 1024 * $(nproc) / $SLURM_CPUS_PER_TASK )"
+let TOTAL_PROCESORS="$(cat /proc/cpuinfo|grep ^processor |wc -l)"
+let MAX_MEMORY_DEFAULT="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / ( (1024 * $TOTAL_PROCESORS) / $SLURM_CPUS_PER_TASK )"
 [ ! -z $SLURM_MEM_PER_CPU ] && let MAX_MEMORY="$SLURM_MEM_PER_CPU * $SLURM_CPUS_PER_TASK" || MAX_MEMORY="$MAX_MEMORY_DEFAULT"
 export MAX_MEMORY_DEFAULT
 export MAX_MEMORY

data/lib/rbbt/persist/tsv/adapter.rb

@@ -132,7 +132,7 @@ module Persist
 
     def read_lock
       read if closed?
-      if read?
+      if read? || write?
         return yield
       end
 

data/lib/rbbt/resource.rb

@@ -6,6 +6,7 @@ require 'set'
 
  
 module Resource
+  class ResourceNotFound < RbbtException; end
 
   class << self
     attr_accessor :lock_dir
@@ -154,16 +155,18 @@ module Resource
       rake_dir, content = rake_for(path)
       rake_dir = Path.setup(rake_dir.dup, self.pkgdir, self)
     else
-      begin
-        if path !~ /\.(gz|bgz)$/
+      if path !~ /\.(gz|bgz)$/
+        begin
+          produce(path.annotate(path + '.gz'), force)
+        rescue ResourceNotFound
           begin
-            produce(path.annotate(path + '.gz'), force)
-          rescue
             produce(path.annotate(path + '.bgz'), force)
+          rescue ResourceNotFound
+            raise ResourceNotFound, "Resource is missing and does not seem to be claimed: #{ self } -- #{ path } "
           end
         end
-      rescue
-        raise "Resource is missing and does not seem to be claimed: #{ self } -- #{ path } "
+      else
+        raise ResourceNotFound, "Resource is missing and does not seem to be claimed: #{ self } -- #{ path } "
       end
     end
 
@@ -174,7 +177,7 @@ module Resource
     end
 
     if type and not File.exist?(final_path) or force
-      Log.medium "Producing: #{ final_path }"
+      Log.medium "Producing: (#{self.to_s}) #{ final_path }"
       lock_filename = Persist.persistence_path(final_path, {:dir => Resource.lock_dir})
 
       Misc.lock lock_filename do

data/lib/rbbt/tsv/csv.rb

@@ -8,6 +8,7 @@ module TSV
     noheaders = ! headers
 
     type = options.delete :type
+    cast = options.delete :cast
     merge = options.delete :merge
     key_field = options.delete :key_field
     fields = options.delete :fields
@@ -46,6 +47,10 @@ module TSV
       else
         key, *values = row
       end
+      
+      if cast
+        values = values.collect{|v| v.send cast }
+      end
 
       case type
       when :double, :flat

data/lib/rbbt/tsv/parser.rb

@@ -40,7 +40,7 @@ module TSV
       # Process fields line
 
       preamble << line if line
-      while line and (TrueClass === @header_hash or (String === @header_hash and Misc.fixutf8(line) =~ /^#{@header_hash}/ ))
+      while line && (TrueClass === @header_hash || (String === @header_hash && Misc.fixutf8(line) =~ /^#{@header_hash}/ ))
         @fields = line.split(@sep, -1)
         @key_field = @fields.shift
         @key_field = @key_field[(0 + header_hash.length)..-1] if String === @header_hash
@@ -49,7 +49,7 @@ module TSV
         line = (@header_hash != "" ?  stream.gets : nil)
         line = Misc.fixutf8 line.chomp if line
         preamble << line if line
-        @header_hash = false if TrueClass === @header_hash
+        @header_hash = false if TrueClass === @header_hash || @header_hash == ""
       end
 
       @preamble = preamble[0..-3] * "\n"

data/lib/rbbt/tsv/stream.rb

@@ -56,6 +56,7 @@ module TSV
       preambles     = []
 
       streams = streams.collect do |stream|
+
         parser = TSV::Parser.new stream, options.dup
         sfields = parser.fields
 

data/lib/rbbt/util/misc/pipes.rb

@@ -43,7 +43,7 @@ module Misc
       File.mkfifo path
       yield path
     ensure
-      FileUtils.rm path if erase
+      FileUtils.rm path if erase && File.exists?(path)
     end
   end
   

data/lib/rbbt/workflow.rb

@@ -187,17 +187,21 @@ module Workflow
       clean_name = wf_name.sub(/::.*/,'')  
       Log.info{"Looking for '#{wf_name}' in '#{clean_name}'"}
       require_workflow clean_name
-      return Misc.string2const Misc.camel_case(wf_name)
+      workflow = Misc.string2const Misc.camel_case(wf_name)
+      workflow.load_documentation
+      return workflow
     end
 
     Log.high{"Loading workflow #{wf_name}"}
     require_local_workflow(wf_name) or 
     (Workflow.autoinstall and `rbbt workflow install #{Misc.snake_case(wf_name)} || rbbt workflow install #{wf_name}` and require_local_workflow(wf_name)) or raise("Workflow not found or could not be loaded: #{ wf_name }")
-    begin
-      Misc.string2const Misc.camel_case(wf_name)
-    rescue
-      Workflow.workflows.last || true
-    end
+    workflow = begin
+                 Misc.string2const Misc.camel_case(wf_name)
+               rescue
+                 Workflow.workflows.last || true
+               end
+    workflow.load_documentation
+    workflow
   end
 
   attr_accessor :description
@@ -596,6 +600,17 @@ module Workflow
         true
       end
     end
+
+    if ! Open.exists?(step.info_file)
+      begin
+        workflow = step.path.split("/")[-3]
+        task_name = step.path.split("/")[-2]
+        workflow = Kernel.const_get workflow
+        step.task = workflow.tasks[task_name.to_sym]
+      rescue
+        Log.exception $!
+      end
+    end
     step
   end
 

data/lib/rbbt/workflow/definition.rb

@@ -74,6 +74,7 @@ module Workflow
   def dep_task(name, workflow, oname, *rest, &block)
     dep(workflow, oname, *rest, &block) 
     extension workflow.tasks[oname].extension if workflow.tasks.include?(oname) unless @extension
+    returns workflow.tasks[oname].result_description if workflow.tasks.include?(oname) unless @result_description 
     task name do
       raise RbbtException, "dependency not found in dep_task" if dependencies.empty?
       dep = dependencies.last

data/lib/rbbt/workflow/doc.rb

@@ -45,10 +45,25 @@ module Workflow
   end
 
   def load_documentation
-    @documentation = Workflow.parse_workflow_doc documentation_markdown
+    return if @documentation
+    @documentation ||= Workflow.parse_workflow_doc documentation_markdown
     @documentation[:tasks].each do |task, description|
-      raise "Documentation for #{ task }, but not a #{ self.to_s } task" unless tasks.include? task.to_sym
-      tasks[task.to_sym].description = description
+      if task.include? "#"
+        workflow, task = task.split("#")
+        workflow = begin
+                     Kernel.const_get workflow
+                   rescue
+                     next
+                   end
+      else
+        workflow = self
+      end
+
+      if workflow.tasks.include? task.to_sym
+        workflow.tasks[task.to_sym].description = description
+      else
+        Log.low "Documentation for #{ task }, but not a #{ workflow.to_s } task" 
+      end
     end
   end
 

data/lib/rbbt/workflow/step.rb

@@ -458,6 +458,10 @@ class Step
   end
 
   def clean
+    if ! Open.exists?(info_file)
+      Log.high "Refusing to clean step with no .info file: #{path}"
+      return self
+    end
     status = []
     status << "dirty" if done? && dirty?
     status << "not running" if ! done? && ! running? 

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

@@ -97,6 +97,7 @@ class Step
         Open.ln_s(value.path, path)
       when type.to_s == "file"
         if String === value && File.exists?(value)
+          value = File.expand_path(value)
           Open.ln_s(value, path)
         else
           value = value.collect{|v| v = "#{v}" if Path === v; v }if Array === value

data/lib/rbbt/workflow/usage.rb

@@ -122,7 +122,7 @@ module Workflow
       last = _prov_tasks(workflow.dep_tree(task_name))
 
       if child
-        description << "->" << task_name.to_s
+        description << "-> " << task_name.to_s
       elsif first
         description << "" << task_name.to_s
       else
@@ -198,7 +198,7 @@ module Workflow
         puts Misc.format_definition_list_item(name.to_s, description, Log.terminal_width, 20, :yellow)
 
         prov_string = prov_string(dep_tree(name))
-        puts Log.color :blue, " ->" + prov_string if prov_string && ! prov_string.empty?
+        puts Misc.format_paragraph Log.color(:blue, "-> " + prov_string) if prov_string && ! prov_string.empty?
       end
 
     else

data/lib/rbbt/workflow/util/archive.rb

@@ -1,6 +1,6 @@
 class Step
 
-  MAIN_RSYNC_ARGS="-avztAXHP"
+  MAIN_RSYNC_ARGS="-avztAXHP --copy-links"
   
   def self.link_job(path, target_dir, task = nil, workflow = nil)
     Path.setup(target_dir)

data/lib/rbbt/workflow/util/trace.rb

@@ -10,6 +10,9 @@ module Workflow
       started = job.info[:started]
       ddone = job.info[:done]
 
+      started = Time.parse started if String === started
+      ddone = Time.parse ddone if String === ddone
+
       code = [job.workflow, job.task_name].compact.collect{|s| s.to_s} * " · "
       code = job.name + " - " + code
 
@@ -70,8 +73,8 @@ module Workflow
 
     start = data.column("Start.second").values.flatten.collect{|v| v.to_f}.min
     eend = data.column("End.second").values.flatten.collect{|v| v.to_f}.max
-    total = eend - start
-    Log.info "Total time elapsed: #{total} seconds"
+    total = eend - start unless eend.nil? || start.nil?
+    Log.info "Total time elapsed: #{total} seconds" if total
 
     data
   end
@@ -140,7 +143,13 @@ rbbt.png_plot('#{plot}', 'plot(timeline)', width=#{width}, height=#{height}, poi
       info = tasks_info[task] ||= IndiferentHash.setup({})
       dep_info = IndiferentHash.setup(dep.info)
 
-      time = dep_info[:done] - dep_info[:started]
+      ddone = dep_info[:done]
+      started = dep_info[:started]
+
+      started = Time.parse started if String === started
+      ddone = Time.parse ddone if String === ddone
+
+      time = ddone - started
       info[:time] ||= []
       info[:time] << time
 
@@ -178,19 +187,25 @@ rbbt.png_plot('#{plot}', 'plot(timeline)', width=#{width}, height=#{height}, poi
     jobs = []
     seed_jobs.each do |step|
       jobs += step.rec_dependencies + [step]
-
       step.info[:archived_info].each do |path,ainfo|
         archived_step = Step.new path
-        class << archived_step
-          self
-        end.define_method :info do
+
+        archived_step.define_singleton_method :info do
           ainfo
         end
+
+        #class << archived_step
+        #  self
+        #end.define_method :info do
+        #  ainfo
+        #end
+
         jobs << archived_step
       end if step.info[:archived_info]
+
     end
 
-    jobs = jobs.uniq.sort_by{|job| t = job.info[:done]; t || Open.mtime(job.path) || 0 }
+    jobs = jobs.uniq.sort_by{|job| t = job.info[:started] || Open.mtime(job.path) || Time.now; Time === t ? t : Time.parse(t) }
 
     data = trace_job_times(jobs, options[:fix_gap])
 
@@ -200,10 +215,10 @@ rbbt.png_plot('#{plot}', 'plot(timeline)', width=#{width}, height=#{height}, poi
 
     raise "No jobs to process" if data.size == 0
 
-    plot, size, width, height = options.values_at :plot, :width, :height
+    plot, size, width, height = options.values_at :plot, :size, :width, :height
 
     size = 800 if size.nil?
-    width = size * 2 if width.nil?
+    width = size.to_i * 2 if width.nil?
     height = size  if height.nil?
 
     plot_trace_job_times(data, plot, width, height) if plot

data/share/rbbt_commands/migrate

@@ -94,12 +94,12 @@ real_paths.each do |source|
   end
 
   if options[:target]
-   target_path = [options[:target], target] * ":" 
+   target_path = [options[:target], "'" + target + "'"] * ":" 
   else
-   target_path = target
+   target_path = "'" + target + "'"
   end
 
-  cmd = "rsync -avztAXHP --copy-unsafe-links #{test_str} #{excludes_str} #{source} #{target_path} #{other * " "}"
+  cmd = "rsync -avztAXHP --copy-unsafe-links #{test_str} #{excludes_str} '#{source}' #{target_path} #{other * " "}"
 
   cmd << " && rm -Rf #{source}" if options[:delete]
 

data/share/rbbt_commands/workflow/forget_deps

@@ -8,9 +8,11 @@ $0 = "rbbt #{$previous_commands*" "} #{ File.basename(__FILE__) }" if $previous_
 
 options = SOPT.setup <<EOF
 
-Make a job forget all its dependencies and archive their meta-data
+Make a job forget its dependencies and archive their meta-data
 
-$ #{$0} [options] <job_path>
+$ #{$0} [options] <job_path> [<task_name>|<workflow>#<task_name>] ...
+
+Specific dependencies can be specified as . Otherwise, all are forgoten.
 
 -h--help Print this help
 -p--purge Purge dependencies
@@ -26,7 +28,7 @@ if options[:help]
   exit 0
 end
 
-path = ARGV[0]
+path, *remove = ARGV
 
 raise ParameterException, "No path given" if path.nil?
 step = Workflow.load_step path
@@ -34,10 +36,20 @@ step = Workflow.load_step path
 step.archive_deps
 step.copy_files_dir
 dependencies = step.dependencies
-step.set_info :dependencies, []
 
-if options[:purge]
+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 } 
+else
+ remove_paths = dependencies.collect{|dep| dep.path }
+end
+
+step.set_info :dependencies, step.info[:dependencies].reject{|info| remove_paths.include? info.last}
+
+if options[:purge] || options[:recursive_purge]
   dependencies.each do |dependency|
+    next unless remove_paths.include? dependency.path
     Step.purge(dependency.path, options[:recursive_purge])
   end
 end

data/test/rbbt/persist/tsv/test_tokyocabinet.rb

@@ -51,7 +51,7 @@ class TestPersistTSVTC < Test::Unit::TestCase
     end
   end
 
-  def test_annotation_persist_with_repeitions
+  def test_annotation_persist_with_repetitions
     TmpFile.with_file do |tmp|
       entity1 = "Entity 1"
       entity2 = "Entity 2"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.31.15
+  version: 5.32.5
 platform: ruby
 authors:
 - Miguel Vazquez
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-04-14 00:00:00.000000000 Z
+date: 2021-04-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -542,7 +542,7 @@ homepage: http://github.com/mikisvaz/rbbt-util
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -557,101 +557,102 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.4
-signing_key: 
+rubyforge_project:
+rubygems_version: 2.7.6
+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/util/test_orchestrator.rb
 - test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/test_schedule.rb
-- test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/step/test_dependencies.rb
+- test/rbbt/workflow/test_schedule.rb
+- test/rbbt/workflow/util/test_orchestrator.rb
 - test/rbbt/workflow/test_task.rb
-- test/rbbt/resource/test_path.rb
-- test/rbbt/util/test_colorize.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_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/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/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/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/util/test_colorize.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/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/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/util/misc/test_omics.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/log/test_progress.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/tsv/test_parser.rb
 - test/rbbt/tsv/test_csv.rb
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_manipulate.rb
 - test/rbbt/tsv/test_field_index.rb
 - test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_stream.rb
 - test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_excel.rb
-- test/rbbt/tsv/parallel/test_through.rb
+- test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_index.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
+- test/rbbt/tsv/parallel/test_through.rb