rbbt-util 5.9.3 → 5.9.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 29daeb012f3ce90b479f7b858abff79e166f936d
-  data.tar.gz: 78e6fd7422a46b33271de8c8f0eb81d0fc97d772
+  metadata.gz: 2cf8e981590ec75d716c3b173786a1d9d49751af
+  data.tar.gz: c48d0c459d08b67b68a5caf94d31bef4ea10e4c4
 SHA512:
-  metadata.gz: bcbb30fb3e53e872d6b2de2fce030f93a78fbe01b7d1a238d8dff243d602f2f42ba6d11e01de4f11ac9aead3d4a90c03779bdd8f1311aa72b4c62d2d320bfef5
-  data.tar.gz: 4e5faf9f1ac86e500fd9f5d747ed2c34ba31aabf2a8bbced66aa626bb7e2f1b7d3428cd5af714dfe09c7ae5990302409edfb691bafe1e7fa4bf99d64c01f4dcc
+  metadata.gz: 7687ee59c28372845dfb2d9d3606c2aa3409fcc299566530dcec737b48ef764bfadb49504d5dd0256fac2f85d8ddf10a5780642034ed6f05ccfa2a73e5b187c1
+  data.tar.gz: f47bb2989be8fa6f39e15551caf8cd35d4506ba07092b61716e6b7a14efff001b5e12509e34266fd572f0f22cef07f4d138cd3e518c4243e6e493792027ab6b6

data/bin/rbbt

@@ -2,6 +2,9 @@
 
 require 'rbbt'
 require 'rbbt/util/simpleopt'
+require 'highline'
+
+Log.tty_size = HighLine::SystemExtensions.terminal_size.first
 
 options = SOPT.setup <<EOF
 Ruby bioinformatics toolkit
@@ -96,13 +99,13 @@ end
 def print_error(error, backtrace = nil)
   puts Log.color :red, "Error:"
   puts
-  puts error
   if backtrace
-    puts
     puts Log.color :red, "Backtrace:"
     puts
-    puts backtrace * "\n"
+    puts backtrace.reverse * "\n"
+    puts
   end
+  puts Log.color :red, error
   puts
 end
 

data/lib/rbbt/persist.rb

@@ -289,7 +289,7 @@ module Persist
             res
           end
         rescue
-          Log.high "Error in persist. #{Open.exists?(path) ? "Erasing '#{ path }'" : ""}"
+          Log.high "Error in persist: #{path}#{Open.exists?(path) ? Log.color(:red, " Erasing") : ""}"
           FileUtils.rm path if Open.exists? path 
           raise $!
         end

data/lib/rbbt/tsv/attach.rb

@@ -197,7 +197,7 @@ module TSV
       attach_source_key other, other.key_field, :fields => fields, :one2one => one2one
     else
       index = TSV.find_traversal(self, other, options)
-      raise "Cannot traverse identifiers" if index.nil?
+      raise FieldNotFoundError, "Cannot traverse identifiers" if index.nil?
       Log.debug "Attachment with index: #{other.key_field}"
       attach_index other, index, fields
     end

data/lib/rbbt/tsv/attach/util.rb

@@ -307,7 +307,7 @@ module TSV
     in_namespace = options[:in_namespace]
 
     identifiers1 = tsv1.identifier_files || []
-    identifiers1 += options[:identifiers] if options[:identifiers]
+    identifiers1 += [options[:identifiers]].flatten if options[:identifiers]
     identifiers2 = tsv2.identifier_files || []
 
     identifiers1.unshift tsv1

data/lib/rbbt/util/log.rb

@@ -13,11 +13,21 @@ module Log
   ERROR    = 6
 
   class << self
-    attr_accessor :logfile, :severity, :nocolor
+    attr_accessor :logfile, :severity, :nocolor, :tty_size
   end
   self.nocolor = ENV["RBBT_NOCOLOR"] == 'true'
 
 
+  def self.with_severity(level)
+    orig = Log.severity
+    begin
+      Log.severity = level
+      yield
+    ensure
+      Log.severity = orig
+    end
+  end
+
   def self.logfile
     @logfile = nil
   end
@@ -39,7 +49,7 @@ module Log
     if str.nil?
       color
     else
-      color + str + self.color(0)
+      color + str.to_s + self.color(0)
     end
   end
 
@@ -103,7 +113,7 @@ module Log
   end
 
   def self.exception(e)
-    error(e.message)
+    error([e.class.to_s, e.message].compact * ": ")
     error("BACKTRACE:\n" + e.backtrace * "\n") 
   end
 

data/lib/rbbt/workflow/accessor.rb

@@ -97,16 +97,17 @@ class Step
   def self.log(status, message, path, &block)
     if block_given?
       start = Time.now
-      Log.medium do 
+      Log.info do 
         now = Time.now
-        str = "#{ Log.color :cyan, status.to_s }"
+        str = Log.color :reset
+        str << "#{ Log.color :cyan, status.to_s }"
         str << ": #{ message }" if message
         str << " -- #{Log.color :blue, path.to_s}" if path
         str
       end
       res = yield
       eend = Time.now
-      Log.medium do 
+      Log.info do 
         now = Time.now
         str = "#{ Log.color :cyan, status.to_s } +#{Log.color :green, "%.1g" % (eend - start)}"
         str << " -- #{Log.color :blue, path.to_s}" if path
@@ -114,9 +115,10 @@ class Step
       end
       res
     else
-      Log.medium do 
+      Log.info do 
         now = Time.now
-        str = "#{ Log.color :cyan, status.to_s }"
+        str = Log.color :reset
+        str << "#{ Log.color :cyan, status.to_s }"
         str << ": #{ message }" if message
         str << " -- #{Log.color :blue, path.to_s}" if path
         str

data/lib/rbbt/workflow/step.rb

@@ -42,7 +42,9 @@ class Step
         attr_accessor :relay_step
         alias original_log log 
         def log(status, message = nil)
-          original_log(status, message)
+          Log.with_severity 10 do
+            original_log(status, message)
+          end
           relay_step.log([task.name.to_s, status.to_s] * ">", message.nil? ? nil : [task.name.to_s, message] * ">")
         end
       end
@@ -104,9 +106,12 @@ class Step
       Open.rm info_file if Open.exists? info_file
 
       set_info :pid, Process.pid
+      set_info :issued, Time.now
 
       set_info :dependencies, dependencies.collect{|dep| [dep.task.name, dep.name]}
+      log(:preparing, "Preparing job")
       dependencies.each{|dependency| 
+        Log.info "#{Log.color :magenta, "Checking dependency"} #{Log.color :yellow, task.name.to_s || ""} => #{Log.color :yellow, dependency.task.name.to_s || ""}"
         begin
           dependency.relay_log self
           dependency.clean if not dependency.done? and dependency.error?
@@ -114,15 +119,12 @@ class Step
         rescue Exception
           backtrace = $!.backtrace
           set_info :backtrace, backtrace 
-          log(:error, "Exception processing dependency #{dependency.path}")
-          log(:error, "#{$!.class}: #{$!.message}")
-          log(:error, "backtrace: #{$!.backtrace.first}")
-          Log.exception $!
-          raise "Exception processing dependency #{dependency.path}"
+          log(:error, "Exception processing dependency #{Log.color :yellow, dependency.task.name.to_s} -- #{$!.class}: #{$!.message}")
+          raise $!
         end
       }
       
-      Log.medium{"#{Log.color :magenta, "Starting task"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}]: #{ path }"}
+      Log.info{"#{Log.color :magenta, "Starting task"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}]: #{ Log.color :blue, path }"}
       set_info :status, :started
 
       set_info :started, (start_time = Time.now)
@@ -157,14 +159,13 @@ class Step
 
               set_info :backtrace, backtrace 
               log(:error, "#{$!.class}: #{$!.message}")
-              log(:error, "backtrace: #{$!.backtrace.first}")
               raise $!
             end
 
       set_info :status, :done
       set_info :done, (done_time = Time.now)
       set_info :time_elapsed, done_time - start_time
-      Log.medium{"#{Log.color :magenta, "Completed task"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}]: #{ path }"}
+      Log.info{"#{Log.color :magenta, "Completed task"} #{Log.color :yellow, task.name.to_s || ""} [#{Process.pid}]: #{ Log.color :blue, path }"}
 
       res
     end

data/lib/rbbt/workflow/usage.rb

@@ -22,19 +22,19 @@ module Task
     puts SOPT.input_doc(inputs, input_types, input_descriptions, input_defaults, true)
     puts
 
-    puts "Returns: " << Log.color(:blue, result_type.to_s) << "\n"
-    puts
-
     if deps and deps.any?
       puts "From dependencies:"
       puts
       deps.each do |dep|
-        puts "  #{dep.name}:"
+        puts "  #{Log.color :magenta, dep.name.to_s}:"
         puts
         puts SOPT.input_doc((dep.inputs - self.inputs), dep.input_types, dep.input_descriptions, dep.input_defaults, true)
         puts
       end
     end
+
+    puts "Returns: " << Log.color(:blue, result_type.to_s) << "\n"
+    puts
   end
 end
 

data/share/rbbt_commands/tsv/info

@@ -44,18 +44,18 @@ else
 
   puts "File: #{ file }"
   puts "Type: #{header.type}"
-  puts "Key: #{header.key_field}"
+  puts "Key: #{Log.color :yellow, header.key_field}"
   puts "Fields: "
   if header.fields.nil?
   else
     header.fields.each_with_index do |f,i|
-      puts "  - #{i + 1}: " << f
+      puts "  - #{Log.color :cyan, i + 1}: " << Log.color(:yellow, f)
     end
   end
-  puts "Rows: #{`wc -l #{ file }|cut -f 1 -d' '`}" unless Open.remote? file
-  puts "First line:"
+  puts "Rows: #{Log.color :blue, `wc -l #{ file }|cut -f 1 -d' '`}" unless Open.remote? file
   parts = []
-  header.first_line.split(header.sep).each_with_index{|p,i| parts << "(#{i}) #{p}"}
+  header.first_line.split(header.sep).each_with_index{|p,i| parts << (Log.color(:cyan, "(#{i}) ") << p.strip) }
   puts parts * "\t"
+  puts
 end
 

data/share/rbbt_commands/workflow/task

@@ -142,7 +142,8 @@ the job dependencies recursively.
 -pf--printpath Print the path of the job result:
 -cl--clean Clean the last step of the job so that it gets recomputed:
 -rcl--recursive_clean Clean the last step and its dependencies to recompute the job completely:
---fork Run job asyncronously:
+--fork Run job asyncronously and monitor progress. It monitors detached processes as well:
+--detach Run job asyncronously and detach process:
 --exec Run job with no persistence:
 -O--output* Save job result into file:
 -jf--job_file* Output one of the job produced files:
@@ -160,6 +161,7 @@ task     = ARGV.shift
 # Set log, fork, clean, recursive_clean and help
 help = !!options.delete(:help)
 do_fork = !!options.delete(:fork)
+detach = !!options.delete(:detach)
 do_exec = !!options.delete(:exec)
 clean = !!options.delete(:clean)
 recursive_clean = !!options.delete(:recursive_clean)
@@ -221,10 +223,12 @@ workflow.workdir = Path.setup(File.expand_path(options.delete(:workdir))) if opt
 
 #- get job
 
+
 job = workflow.job(task.name, name, job_options)
 
 # clean job
 if clean 
+  job.abort if job.running?
   job.clean 
   sleep 1
   job = workflow.job(task.name, name, job_options)
@@ -262,21 +266,33 @@ begin
 
   if do_fork
     job.fork
+    if detach
+      Process.detach job.pid
+      puts Log.color(:magenta, "Issued: ") + Log.color(:magenta, job.pid.to_s) + ' -- ' + job.path
+      exit 0
+    end
     puts 
+    puts
     while not job.done?
-      message = job.messages ? job.messages.last : "no message"
-      status = job.status
-      puts("No status yet") and next if status.nil?
-      puts Log.return_line + "Waiting on #{job.pid} " + [Log.color(:magenta, status.to_s),message]*" " + " " * 100
+      message = (job.messages and job.messages.any?) ? job.messages.last.strip : "no message"
+      status = job.status || "no status"
+      time = Time.now - job.info[:issued] if job.info and job.info.include? :issued
+      size = Log.tty_size
+      size = 100 if size.nil?
+      puts Log.return_line << " " * size << Log.return_line 
+      puts Log.return_line << " " * size << Log.return_line 
+      puts "#{Log.color :blue, job.path}"
+      puts "Waiting on #{Log.color :blue, job.info[:pid] || job.pid} (+#{time.to_i if time}) " << [Log.color(:cyan, status.to_s),message.strip].compact*" " 
       sleep 2
     end
-    Signal.trap(:INT){ job.abort }
+    #Signal.trap(:INT){ job.abort }
     raise job.messages.last if job.error?
     res = job.load
   else
     res = job.run(true)
   end
 
+  puts res
 
   if options.delete(:provenance)
     pp job.provenance
@@ -306,7 +322,6 @@ rescue ParameterException
   exit -1
 end
 
-
 if options.delete(:list_job_files)
   out.puts job.files * "\n"
   exit 0
@@ -317,8 +332,9 @@ if job_file = options.delete(:job_file)
   out.puts Path === file ? file.read : file
   exit 0
 end
+ddd 1
 
-if Step === res
+if Step === res and not res.exec
   out.puts Open.read(res.path) if File.exists? res.path
 else
   out.puts res

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.9.3
+  version: 5.9.4
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-20 00:00:00.000000000 Z
+date: 2014-03-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake