scout-gear 10.11.6 → 10.11.7

data/scout_commands/alias

@@ -17,7 +17,7 @@ earlier, like --dev or --log. Edit #{Scout.ect.cmd_alias.find} to fine tune.
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/batch/clean

@@ -25,7 +25,7 @@ $ #{$0} [<options>] <filename> [<other|->]*
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end
@@ -109,7 +109,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
  end
 
  if File.exist?(fstatus = File.join(dir, 'job.status'))
-   fstatus_txt = Open.read(fstatus) 
+   fstatus_txt = Open.read(fstatus)
    begin
      if job_batch_system == "lsf"
        nodes = Open.read(fstatus).split("\n").last.split(/\s+/)[5].split(",")
@@ -140,28 +140,28 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
  aborted = error = true if ! done && aborted.nil? && error.nil?
  #if done || error || aborted || running || queued || jobid || search
  #  select = false
- #  select = true if done && exit_status && exit_status.to_i == 0 
- #  select = true if error && exit_status && exit_status.to_i != 0 
+ #  select = true if done && exit_status && exit_status.to_i == 0
+ #  select = true if error && exit_status && exit_status.to_i != 0
  #  select = true if aborted && (exit_status.nil? && ! running_jobs.include?(id))
- #  select = select && jobid.split(",").include?(id) if jobid 
+ #  select = select && jobid.split(",").include?(id) if jobid
  #  select = select && cmd.match(/#{search}/) if search
- #  next unless select 
+ #  next unless select
  #end
 
- if done || error || aborted || queued || jobid 
+ if done || error || aborted || queued || jobid
    select = false
    select = true if done && exit_status == 0
-   select = true if error && exit_status && exit_status != 0 
+   select = true if error && exit_status && exit_status != 0
    select = true if aborted && (exit_status.nil? && ! running_jobs.include?(id))
    is_running =  exit_status.nil? && ( (running_jobs.include?(id) && (!deps || (running_jobs & deps).empty?)) || different_system )
    select = true if queued && deps && (running_jobs & deps).any? || queued && is_running && nodes.empty?
    select = true if jobid && jobid.split(",").include?(id)
    select = select && cmd.match(/#{search}/) if search
-   next unless select 
+   next unless select
  elsif search
    select = false
    select = true if search && cmd.match(/#{search}/)
-   next unless select 
+   next unless select
  end
 
 
@@ -180,7 +180,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
 
  if options[:batch_parameters]
    puts Log.color(:magenta, "BATCH parameters: ")
-   case job_batch_system 
+   case job_batch_system
    when 'slurm'
      puts Log.color :blue, CMD.cmd('grep "^#SBATCH" |tail -n +6', :in => Open.read(fcmd)).read.strip
    when 'lsf'
@@ -206,6 +206,6 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
  Open.rm_rf dir unless dry_run
 end
 
-puts 
+puts
 puts "Found #{count} jobs"
 

data/scout_commands/batch/list

@@ -12,7 +12,7 @@ List all batch jobs
 
 $ #{$0} [<options>] <filename> [<other|->]*
 
-$ rbbt slurm list [options] 
+$ rbbt slurm list [options]
 
 -h--help Print this help
 -d--done Done jobs only
@@ -33,7 +33,7 @@ $ rbbt slurm list [options]
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end
@@ -132,7 +132,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
   end
 
   if File.exist?(fstatus = File.join(dir, 'job.status'))
-    fstatus_txt = Open.read(fstatus) 
+    fstatus_txt = Open.read(fstatus)
     begin
       if job_batch_system == "lsf"
         nodes = Open.read(fstatus).split("\n").last.split(/\s+/)[5].split(",")
@@ -170,47 +170,47 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
   cadeps = Open.read(fcadep).split("\n") if File.exist?(fcadep)
 
   is_running =  exit_status.nil? && ( (running_jobs.include?(id) && (deps.nil? || (running_jobs & deps).empty?)) || different_system )
-  if done || error || aborted || running || queued || jobid 
+  if done || error || aborted || running || queued || jobid
     select = false
     select = true if done && exit_status == 0
-    select = true if error && exit_status && exit_status != 0 
+    select = true if error && exit_status && exit_status != 0
     select = true if aborted && (exit_status.nil? && ! running_jobs.include?(id))
     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 && step_path.match(/#{search}/) if search
-    next unless select 
+    next unless select
   elsif search
     select = false
     select = true if search && cmd.match(/#{search}/)
-    next unless select 
+    next unless select
   end
 
 
   count += 1
 
   if options[:compressed] && tail.nil?
-    status = exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) :  Log.color(:green, id)  
+    status = exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) :  Log.color(:green, id)
     if different_system
-      status = exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" :  Log.color(:green, id)  
+      status = exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" :  Log.color(:green, id)
     else
       #status = exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" :  (running_jobs.include?(id) || $norunningjobs ? Log.color(:green, id) : Log.color(:red, id) )
-      status = exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" : 
-        (running_jobs.include?(id) || $norunningjobs ? 
-         (is_running ? Log.color(:cyan, id) : Log.color(:yellow, id) ) : 
+      status = exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" :
+        (running_jobs.include?(id) || $norunningjobs ?
+         (is_running ? Log.color(:cyan, id) : Log.color(:yellow, id) ) :
          Log.color(:red, id) )
-    end 
+    end
     prog_rep = []
-    if options[:progress] 
+    if options[:progress]
       step_line = Open.read(fcmd).split("\n").select{|line| line =~ /^#STEP_PATH:/}.first
       if step_line
         step_path = step_line.split(": ").last.strip
         step = Step.new step_path
         has_bar = false
         [step].reverse.each do |j|
-          next if j.done? 
+          next if j.done?
           if j.file(:progress).exists?
-            bar = Log::ProgressBar.new 
+            bar = Log::ProgressBar.new
             bar.load(j.file(:progress).yaml)
             rep = bar.report_msg.split("·")[1]
             rep = rep.sub(/.*?(\d+%)/, Log.color(:blue,'\1')).sub(/\-.*/,'')
@@ -238,7 +238,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
     puts Log.color(:magenta, "Job ID (#{Log.color(:red, job_batch_system)}): ") << (exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" :  Log.color(:green, id)  )
   else
     puts Log.color(:magenta, "Job ID: ") << (exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" :  (running_jobs.include?(id) || $norunningjobs ? Log.color(:green, id) : Log.color(:red, id) ))
-  end 
+  end
   puts Log.color(:magenta, "Dependencies: ") << deps * ", " if deps
   puts Log.color(:magenta, "Dependencies (can fail): ") << cadeps * ", " if cadeps
   puts Log.color(:magenta, "Nodes: ") << nodes * ", " if long
@@ -247,7 +247,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
 
   if options[:batch_parameters]
     puts Log.color(:magenta, "BATCH parameters: ")
-    case job_batch_system 
+    case job_batch_system
     when 'slurm'
       text = CMD.cmd('grep "^#SBATCH" ', :in => Open.read(fcmd)).read.strip
     when 'lsf'
@@ -295,14 +295,14 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
     ticks = 1 if ticks == 0
     time_elapsed = 1 if time_elapsed == 0
     puts Log.color(:yellow, "CPU average: ") + "%.2f" % ( ticks / clock_ticks / time_elapsed * 100).to_s
-    puts Log.color(:yellow, "RSS average: ") + "%.2f GB" % Misc.mean(rss_average.collect{|t,l| Misc.sum(l) / (1024 * 1024 * 1024)}).to_s 
+    puts Log.color(:yellow, "RSS average: ") + "%.2f GB" % Misc.mean(rss_average.collect{|t,l| Misc.sum(l) / (1024 * 1024 * 1024)}).to_s
     puts Log.color(:yellow, "Time: ") + Misc.format_seconds((eend - start))
 
   end
 
   if options[:sacct_peformance]
     begin
-      raise "sacct not supported for LSF" unless batch_system == 'slurm' 
+      raise "sacct not supported for LSF" unless batch_system == 'slurm'
       tsv = TSV.open(CMD.cmd("sacct -j #{id} -o 'jobid,AveRSS,MaxRSS,MaxDiskRead,MaxDiskWrite' -P|grep 'JobID\\|\.batch'"), :header_hash => '', :sep => "|", :type => :list)
       values = tsv[tsv.keys.first]
       if values.compact.any?
@@ -324,20 +324,21 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
       puts CMD.cmd("grep -i -w 'Completed step' #{File.join(dir, 'std.err')} | grep -v 'Retrying dep.' | tail -n #{tail.to_i}", :no_fail => true).read
     else
       puts Log.color(:magenta, "Log tail: ")
-      puts CMD.cmd(" cat #{File.join(dir, 'std.err')} | grep -v '^[^\\s:]*\\[3.m'  | grep -v -e '^[[:space:]]*$' | grep -v  \"\\(STDOUT\\|STDERR\\):[[:space:]]*$\" | tail -n #{tail.to_i} ").read
+      pad_tail = 1000 + tail.to_i
+      puts CMD.cmd("tail -n #{pad_tail} #{File.join(dir, 'std.err')} | grep -v '^[^\\s:]*\\[3.m'  | grep -v -e '^[[:space:]]*$' | grep -v  \"\\(STDOUT\\|STDERR\\):[[:space:]]*$\" | tail -n #{tail.to_i} ").read
     end
   end
 
-  if options[:progress] 
+  if options[:progress]
     step_line = Open.read(fcmd).split("\n").select{|line| line =~ /^#STEP_PATH:/}.first
     if step_line
       step_path = step_line.split(": ").last.strip
       step = Step.new step_path
       has_bar = false
       (step.rec_dependencies.to_a + [step]).reverse.each do |j|
-        next if j.done? 
+        next if j.done?
         if j.file(:progress).exists?
-          bar = Log::ProgressBar.new 
+          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
@@ -352,6 +353,6 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
 
 end
 
-puts 
+puts
 puts Log.color :clear, "Found #{count} jobs"
 

data/scout_commands/batch/tail

@@ -8,14 +8,14 @@ options = SOPT.setup <<EOF
 
 Queue a job in Marenostrum
 
-$ rbbt slurm tail <directory|jobid> [options] 
+$ rbbt slurm tail <directory|jobid|step> [options]
 
 -h--help Print this help
 EOF
 
 if options[:help]
  if defined? rbbt_usage
-  rbbt_usage 
+  rbbt_usage
  else
   puts SOPT.doc
  end
@@ -29,18 +29,22 @@ directory = ARGV.shift
 
 raise ParameterException if directory.nil?
 
+workdir = File.expand_path('~/scout-batch')
+Path.setup(workdir)
+
 if directory =~ /^[0-9]*$/
-  workdir = File.expand_path('~/scout-batch')
-  Path.setup(workdir)
 
   workdir.glob("**/job.id").each do |file|
     next unless directory == Open.read(file).strip
     directory = File.dirname(file)
     break
   end
+elsif ! File.exist?(File.join(directory, 'command.batch'))
+  out = CMD.cmd("grep -r -l 'STEP_PATH: .*#{directory}' '#{workdir}'").read.split("\n").first
+  directory = out.sub("/command.batch", '') if out and not out.empty?
 end
 
-raise ParameterException, "Could not identify job #{directory}" unless File.exist?(directory)
+raise ParameterException, "Could not identify job #{directory}" unless File.exist?(File.join(directory, 'command.batch'))
 
 require 'rbbt/hpc/slurm'
 

data/scout_commands/cat

@@ -17,7 +17,7 @@ $ #{$0} [<options>] (<resource> <path>|<path>)
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/doc

@@ -16,7 +16,7 @@ If you don't specify the module it prints those available
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end
@@ -26,7 +26,7 @@ end
 
 module_name = ARGV.first
 if module_name.nil?
-  puts Scout.doc.lib.scout.glob("**/*.md").collect{|f| 
+  puts Scout.doc.lib.scout.glob("**/*.md").collect{|f|
     f.find.unset_extension.sub(Scout.doc.lib.scout.find + "/", '')
   } * "\n"
 else

data/scout_commands/entity

@@ -21,7 +21,7 @@ type, property, entity = ARGV
 
 if options[:help] and type.nil?
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end
@@ -63,12 +63,12 @@ end
 entity_module = Kernel.const_get type
 
 entity_module.annotations.uniq.each do |attr|
-  SOPT.register attr.slice(0,1).to_s, attr, true, "Entity attribute" 
+  SOPT.register attr.slice(0,1).to_s, attr, true, "Entity attribute"
 end
 
 if options[:help] and property.nil?
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end
@@ -99,7 +99,7 @@ if options[:help]
   end * " "
 
   SOPT.synopsys['[<property_parameters>]*'] = property_str
-  
+
   if defined? scout_usage
     scout_usage
   else

data/scout_commands/find

@@ -17,7 +17,7 @@ $ #{$0} [<options>] (<resource> <path>|<path>)
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/kb/config

@@ -18,7 +18,7 @@ $ #{$0} [<options>] <name> [knowledge_base]
 EOF
 if options.delete :help
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/kb/entities

@@ -16,7 +16,7 @@ $ #{$0} [<options>] <entity> <identifier_files>
 EOF
 if options.delete :help
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/kb/list

@@ -16,7 +16,7 @@ $ #{$0} [<options>] <filename> [<other|->]*
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/kb/query

@@ -21,7 +21,7 @@ $ #{$0} [<options>] <name> <entity>
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end
@@ -70,7 +70,7 @@ if matches.any?
   else
     matches.each do |match|
       puts Log.color :magenta, (reverse ? match.invert : match)
-      puts index[match].prety_print 
+      puts index[match].prety_print
     end
   end
 else

data/scout_commands/kb/register

@@ -23,7 +23,7 @@ $ #{$0} [<options>] <name> <filename>
 EOF
 if options.delete :help
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/kb/show

@@ -16,7 +16,7 @@ $ #{$0} [<options>] <name>
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/kb/traverse

@@ -20,7 +20,7 @@ $ #{$0} [<options>] <traversal>
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/log

@@ -23,7 +23,7 @@ NONE
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end
@@ -31,11 +31,11 @@ if options[:help]
 end
 
 if ARGV.empty?
-  if Scout.etc.log_severity.exists?                                                                                                                                                         
-    puts Scout.etc.log_severity.read                                                                                                                                                      
-  else                                                                                                                                                                                     
-    puts Scout.etc.log_severity.find + ' does not exist'                                                                                                                                  
-  end                                                                                                                                                                                      
+  if Scout.etc.log_severity.exists?
+    puts Scout.etc.log_severity.read
+  else
+    puts Scout.etc.log_severity.find + ' does not exist'
+  end
 else
   level = ARGV[0]
   level = %w(DEBUG LOW MEDIUM HIGH INFO WARN ERROR NONE)[level.to_i] if level =~ /^\d+$/

data/scout_commands/resource/produce

@@ -8,7 +8,7 @@ options = SOPT.setup <<EOF
 
 Produce a resource
 
-$ #{$0} [<options>] <Resource> <file> 
+$ #{$0} [<options>] <Resource> <file>
 
 -h--help Print this help
 -W--workflows* Workflows to use; 'all' for all in Scout.etc.workflows:
@@ -17,7 +17,7 @@ $ #{$0} [<options>] <Resource> <file>
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/resource/sync

@@ -19,7 +19,7 @@ Path map defaults to :user
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/system/clean

@@ -47,7 +47,7 @@ if locks.any?
   locks.each do |file,info|
     if force or (info[:pid] && ! Misc.pid_alive?(info[:pid]))
       puts "  Removing #{ file }"
-      File.unlink file 
+      File.unlink file
     end
   end
 end
@@ -59,7 +59,7 @@ if persists.any?
   persists.each do |file,info|
     if force or (info[:pid] and Misc.pid_alive? info[:pid])
       puts "  Removing #{ file }"
-      File.unlink file 
+      File.unlink file
     end
   end
 end
@@ -71,7 +71,7 @@ if sensiblewrites.any?
   sensiblewrites.each do |file,info|
     if force or (info[:pid] and Misc.pid_alive? info[:pid])
       puts "  Removing #{ file }"
-      File.unlink file 
+      File.unlink file
     end
   end
 end
@@ -134,13 +134,13 @@ TSV.traverse jobs do |file,i|
     end
   end
 
-  if (force && status !~ /done/) or 
+  if (force && status !~ /done/) or
       status =~ /\b(old|dirty|nopid|error|missing|aborted|dead|sync|waiting)$/ or
       (status == "noinfo" and not done) or
-      status == "" 
+      status == ""
 
-    puts "  Removing #{ file } - #{status}" 
-    Step.clean(file) 
+    puts "  Removing #{ file } - #{status}"
+    Step.clean(file)
   end
 end
 

data/scout_commands/system/status

@@ -177,7 +177,7 @@ workflows.sort.each do |workflow,tasks|
       if options[:quick] and i[:done]
         status = 'done'
         str << " #{ Step.prov_status_msg status }"
-        if inputs and inputs.any? 
+        if inputs and inputs.any?
           str << input_msg(file, inputs)
         end
 
@@ -210,15 +210,15 @@ workflows.sort.each do |workflow,tasks|
         status = status.to_s
         if status != "done" and pid and not Misc.pid_alive?(pid)
           if File.exist? file
-            status << Log.color(:red, " (out of sync)") 
+            status << Log.color(:red, " (out of sync)")
           else
-            status << Log.color(:red, " (dead)") 
+            status << Log.color(:red, " (dead)")
           end
         end
         str << " #{ Step.prov_status_msg status }"
         str << " (dirty)" if status == 'done' && Step.new(file).dirty?
 
-        if inputs and inputs.any? 
+        if inputs and inputs.any?
           str << input_msg(file, inputs)
         end
 

data/scout_commands/template

@@ -19,7 +19,7 @@ Print a template making the substitutions that follow
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/update

@@ -16,7 +16,7 @@ If no gem is specified 'scout-gear' is selected.
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/workflow/info

@@ -16,7 +16,7 @@ $ #{$0} [<options>] <step_path>
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/workflow/install

@@ -22,7 +22,7 @@ workflows install automatically as required.
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/workflow/list

@@ -8,13 +8,13 @@ options = SOPT.setup <<EOF
 
 List all workflows
 
-$ #{$0} [<options>] 
+$ #{$0} [<options>]
 
 -h--help Print this help
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end

data/scout_commands/workflow/process

@@ -22,7 +22,7 @@ $ #{$0} [<options>] ([<workflow>] [<task>] [<name>] | <filename>)
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end
@@ -69,7 +69,7 @@ begin
   end
 
   jobs = files.collect{|file| Workflow.queue_job(file) }
-  
+
 
   begin
     Workflow.produce(jobs, **options)

data/scout_commands/workflow/prov

@@ -19,7 +19,7 @@ $ #{$0} [<options>] <filename> [<other|->]*
 EOF
 if options[:help]
   if defined? scout_usage
-    scout_usage 
+    scout_usage
   else
     puts SOPT.doc
   end
@@ -77,10 +77,10 @@ def adjacency(step)
     info[:dependencies].each do |task,name,path|
       dep = get_step path
       _id, _edges, _node_info = adjacency(dep)
-      edges << [_id, id] 
+      edges << [_id, id]
       edges.concat _edges
       node_info.merge!(_node_info)
-    end 
+    end
   end
 
   [id, edges, node_info]