rbbt-util 5.14.12 → 5.14.14

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 5531ca7de68fb6d150d7e616e9bea2b0bd6a9ca7
+  metadata.gz: 12a27683f6ea8562a740927dac6dca9e22854834
+  data.tar.gz: 6d69aab1d30fa8d56fc8b579a241779e3d84054c
 SHA512:
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-  data.tar.gz: 4bb412bb30f2b17014d7ce818ec71754335ffe12c89494893fe29a3045a666277404e1109280e42debf751bf8415a7d291096dc5f599a5cf48553452e6f8cb15
+  metadata.gz: 7e33da494e19497c5f1aaaca0a6bd35f32edf91d66dbbc2f6b7cfc9932e381bb4ca08ad703b85d5fde85d5c4cba483a48d2ea287ab5e83c5f4d4a82d4f174833
+  data.tar.gz: 8fafdc22a685ce746ceb13cf10c6162c27afbcc51478c241a2d10402d904655b1c2e348e636758ac29cdcb48a3bf7ce9f3c6f4b50fecb45d895780308b8ff172

data/bin/rbbt

@@ -205,6 +205,10 @@ rescue ParameterException
   print_error($!.message, $!.backtrace)
   puts
   exit -1
+rescue SystemExit
+  Log.exception $! unless $?.success?
+rescue Exception
+  Log.exception $!
 ensure
   if options[:profile]
     result = RubyProf.stop

data/lib/rbbt/annotations/annotated_array.rb

@@ -90,28 +90,6 @@ module AnnotatedArray
     end
   end
 
-  def select(method = nil, *args)
-
-    if method
-
-      res = self.zip( self.send(method, *args) ).
-        select{|e,result| result }. 
-        collect{|element,r| element }
-    else
-
-      return self unless block_given?
-
-      res = []
-      each do |value|
-        res << value if yield(value)
-      end
-    end
-
-    annotate(res)
-    res.extend AnnotatedArray 
-
-    res
-  end
 
   def reject
     res = []

data/lib/rbbt/association/item.rb

@@ -62,11 +62,12 @@ module AssociationItem
   end
 
   property :tsv => :array do
-    fields = self.info_fields
+    info_fields = self.info_fields
+    fields = [self.source_type, self.target_type].concat info_fields
     type = [self.source_type, self.target_type] * "~"
     tsv = TSV.setup({}, :key_field => type, :fields => fields, :type => :list, :namespace => self.namespace)
     self.each do |match|
-      tsv[match] = match.info.values_at *fields
+      tsv[match] = [match.source, match.target].concat match.info.values_at(*info_fields)
     end
     tsv
   end
@@ -94,4 +95,38 @@ module AssociationItem
 
     defined?(TSV)? TSV.setup(matrix, :key_field => (key_field || "Source") , :fields => targets, :type => :list) : matrix
   end
+
+  def self._select_match(orig, elem)
+    if Array === orig and Array === elem
+      (orig & elem).any?
+    elsif Array === orig
+      orig.include? elem
+    elsif Array === elem
+      elem.include? orig
+    else
+      elem === orif
+    end
+    false
+  end
+
+  def self.select(list, method = nil, &block)
+    if method and method.any?
+      list.select do |item|
+        method.collect do |key,value|
+          case key
+          when :target
+            _select_match item.target, value
+          when :source
+            _select_match item.source, value
+          else
+            orig = item.info[key]
+            orig = orig.split(";;") if String orig
+            _select_match orig, value 
+          end
+        end
+      end
+    else
+      list.select(&block)
+    end
+  end
 end

data/lib/rbbt/persist.rb

@@ -38,7 +38,10 @@ module Persist
     check = persist_options[:check]
     if not check.nil?
       if Array === check
-        return false if check.select{|file| newer? path, file}.any?
+        if check.select{|file| newer? path, file}.any?
+          Log.medium "Persistence check for #{path} failed in: #{ check.select{|file| newer? path, file} * ", "}"
+          return false 
+        end
      else
         return false if newer? path, check
      end

data/lib/rbbt/resource/rake.rb

@@ -49,8 +49,7 @@ module Rake
         end
       rescue
         Log.error "Error in rake: #{$!.message}"
-        Log.exception $!
-        raise $!
+        Kernel.exit! -1
       end
     }
     Process.waitpid(pid)

data/lib/rbbt/tsv/accessor.rb

@@ -235,14 +235,25 @@ module TSV
 
   def zip_new(key, values)
     values = [values] unless Array === values
-    if self.include? key
-      new = []
-      self[key, true].each_with_index do |v,i|
-        new << (v << values[i])
+    case type
+    when :double
+      if self.include? key
+        new = []
+        self[key, true].each_with_index do |v,i|
+          new << (v << values[i])
+        end
+        self[key] == new
+      else
+        self[key] = values.collect{|v| [v] }
+      end
+    when :flat
+      if self.include? key
+        self[key] = (self[key] + values).uniq
+      else
+        self[key] = values
       end
-      self[key] == new
     else
-      self[key] = values.collect{|v| [v] }
+      raise "Cannot zip_new for type: #{type}"
     end
   end
 

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -294,12 +294,13 @@ module TSV
       Log.medium{"Aborted traversing 2 #{stream_name(obj)}"}
     rescue Exception
       Log.medium{"Exception traversing #{stream_name(obj)}"}
-      Log.exception $!
       begin
         stream = obj_stream(obj)
         stream.abort if stream and stream.respond_to? :abort
         stream = obj_stream(options[:into])
         stream.abort if stream.respond_to? :abort
+      rescue Exception
+      ensure
         raise $!
       end
     end
@@ -378,19 +379,28 @@ module TSV
       return
     end
     begin
+      return false if value.nil?
       case store
-      when Hash
-        return false if value.nil?
-        if Hash === value
-          if TSV === store and store.type == :double
+      when TSV
+        if store.type == :double or store.type == :flat
+          case value
+          when TSV, Hash
             store.merge_zip value
           else
-            store.merge! value
+            store.zip_new *value
           end
         else
           k,v = value
           store[k] = v
         end
+      when Hash
+        case value
+        when TSV, Hash
+          store.merge! value 
+        else
+          k,v = value
+          store[k] = v
+        end
       when TSV::Dumper
         return false if value.nil?
         store.add *value

data/lib/rbbt/util/log.rb

@@ -213,9 +213,8 @@ module Log
 
   def self.exception(e)
     stack = caller
-    error("#{Log.color :error, "EXCEPTION:"} " << stack.first)
-    error([e.class.to_s, e.message].compact * ": ")
-    error("BACKTRACE:\n" + e.backtrace * "\n") 
+    error([e.class.to_s, e.message].compact * ": " )
+    error("BACKTRACE: " << Log.last_caller(caller) << "\n" + color_stack(e.backtrace)*"\n")
   end
 
   def self.color_stack(stack)

data/lib/rbbt/workflow.rb

@@ -297,7 +297,9 @@ module Workflow
       step_path = step_path taskname, jobname, input_values, dependencies, task.extension
     end
 
-    get_job_step step_path, task, input_values, dependencies
+    job = get_job_step step_path, task, input_values, dependencies
+    job.clean_name = jobname
+    job
   end
 
   def load_step(path)

data/lib/rbbt/workflow/accessor.rb

@@ -54,10 +54,6 @@ class Step
     path.sub(/.*\/#{Regexp.quote task.name.to_s}\/(.*)/, '\1')
   end
 
-  def clean_name
-    name.sub(/(.*)_.*/, '\1')
-  end
-
   def task_name
     @task_name ||= task.name
   end
@@ -505,13 +501,17 @@ module Workflow
           case v
           when Symbol
             rec_dependency = real_dependencies.collect{|d| [d, d.dependencies].flatten}.flatten.select{|d| d.task.name == v }.first
-            rec_dependency = rec_dependency.run(true).grace.join.load unless (dependency.first.tasks[dependency[1]].input_options[i] || {})[:stream]
-            inputs[i] = rec_dependency
+            if (dependency.first.tasks[dependency[1]].input_options[i] || {})[:stream]
+              inputs[i] = rec_dependency.run(true).grace.join.path 
+            else
+              inputs[i] = rec_dependency.run(true).join.load
+            end
           else
             inputs[i] = v
           end
         } if options
-        dependency.first.job(dependency[1], jobname, inputs)
+        res = dependency.first.job(dependency[1], jobname, inputs)
+        res
       when Step
         dependency
       when Symbol

data/lib/rbbt/workflow/definition.rb

@@ -40,7 +40,10 @@ module Workflow
       @dependencies << dependency_list
     else
       @dependency_list ||= []
-      dependency_list << block if block_given?
+      if block_given?
+        dependency_list.unshift self if dependency_list.length == 1
+        dependency_list << block 
+      end
       dependencies.concat dependency_list
     end
   end
@@ -48,6 +51,7 @@ module Workflow
   def dep(*dependency, &block)
     @dependencies ||= []
     if block_given?
+      dependency.unshift self if dependency.length == 1
       DependencyBlock.setup block, dependency if dependency.any?
       @dependencies << block
     else

data/lib/rbbt/workflow/step.rb

@@ -5,7 +5,7 @@ require 'rbbt/util/semaphore'
 require 'rbbt/workflow/accessor'
 
 class Step
-  attr_accessor :path, :task, :inputs, :dependencies, :bindings
+  attr_accessor :clean_name, :path, :task, :inputs, :dependencies, :bindings
   attr_accessor :pid
   attr_accessor :exec
   attr_accessor :result, :mutex, :seen
@@ -22,9 +22,16 @@ class Step
     end
   end
 
-  def initialize(path, task = nil, inputs = nil, dependencies = nil, bindings = nil)
+  def clean_name
+    @clean_name ||= begin
+                      info[:clean_name] || path.sub(/_[a-z0-9]{32}/, '')
+                    end
+  end
+
+  def initialize(path, task = nil, inputs = nil, dependencies = nil, bindings = nil, clean_name = nil)
     path = Path.setup(Misc.sanitize_filename(path)) if String === path
-    pat = path.call if Proc === path
+    path = path.call if Proc === path
+
     @path = path
     @task = task
     @bindings = bindings
@@ -39,7 +46,7 @@ class Step
     @mutex = Mutex.new
     @info_mutex = Mutex.new
     @inputs = inputs || []
-    NamedArray.setup @inputs, task.inputs.collect{|s| s.to_s} if task and task.inputs
+    NamedArray.setup @inputs, task.inputs.collect{|s| s.to_s} if task and task.respond_to? :inputs and task.inputs
   end
 
   def inputs
@@ -204,9 +211,13 @@ class Step
 
   def step(name)
     @steps ||= {}
-    @steps[name] ||= rec_dependencies.select do |step| 
-      step.task_name.to_sym == name.to_sym
-    end.first
+    @steps[name] ||= begin
+                       deps = rec_dependencies.select{|step| 
+                         step.task_name.to_sym == name.to_sym
+                       }
+                       deps.first
+                     end
+
   end
 end
 

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

@@ -123,15 +123,14 @@ class Step
     dependencies.uniq.each do |dependency| 
       next if seen.collect{|d| d.path}.include?(dependency.path)
       dependency.seen = seen
-      @seen << dependency
       @seen.concat dependency.rec_dependencies.collect{|d| d } 
+      @seen << dependency
       @seen.uniq!
     end
 
     @seen.each do |dependency|
       next if dependency == self
       next unless dependencies.include? dependency
-      #dependency.relay_log self
       dependency.dup_inputs
     end
 
@@ -147,8 +146,8 @@ class Step
           dependency.clean if (dependency.error? or dependency.aborted? or dependency.status.nil? or not (dependency.done? or dependency.running?))
         end
 
-        unless dependency.started? #dependency.result or dependency.done?
-          dependency.run(true)#.grace
+        unless dependency.started? 
+          dependency.run(true)
         end
       rescue Aborted
         Log.error "Aborted dep. #{Log.color :red, dependency.task.name.to_s}"
@@ -183,6 +182,7 @@ class Step
             :pid => Process.pid,
             :issued => Time.now,
             :name => name,
+            :clean_name => clean_name,
             :dependencies => dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]},
           })
 

data/share/rbbt_commands/workflow/knowledge_base

@@ -51,18 +51,17 @@ when :subset
   source_entities = options[:source_entities] || :all
   target_entities = options[:target_entities] || :all
 
-  source_entities = source_entities.split(/,\|/) if String === source_entities
-  target_entities = target_entities.split(/,\|/) if String === target_entities
+  source_entities = source_entities.split(/[,|]/) if String === source_entities
+  target_entities = target_entities.split(/[,|]/) if String === target_entities
 
   if options[:identify]
-    source_entities = knowledge_base.identify(database, source_entities)
-    target_entities = knowledge_base.identify(database, target_entities)
+    source_entities = knowledge_base.identify_source(database, source_entities)
+    target_entities = knowledge_base.identify_target(database, target_entities)
   end
   entities = {source_format => source_entities, target_format => target_entities}
 
   matches = knowledge_base.subset(database, entities)
 
-
   if options[:tsv]
     puts matches.tsv.to_s
   else

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.14.12
+  version: 5.14.14
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-20 00:00:00.000000000 Z
+date: 2014-08-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake