rbbt-util 5.17.0 → 5.17.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 0c5c8378d8a78fe1341c17cad09d88652714899c
+  metadata.gz: 1ac03b5ef9630246419ee1b188f942ce49b51b5c
+  data.tar.gz: 7334d42c5ca19a5927a0ffb842b2cbac3f75517e
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+  metadata.gz: 04a74c22d7618b91ae8d8ea1e1eea99f05cb667aee28fecc0b66ce426f73bb112a844cb1509b7ad8af4d87bf6ea3005d148a817427c7470b4cba9a73d149ee3d
+  data.tar.gz: 88954c0d848fafd43e5c2defc0b8d490ebb1b3d21d3ab2a5a4dae54cc45dd23a3b9d2e457cc4854b640045006df255cbb0de49bde84f05baf7fcae7b91668424

data/lib/rbbt/association/open.rb

@@ -20,7 +20,7 @@ module Association
 
     data = Persist.persist_tsv(file, "Association Database", options, persist_options) do |data|
       options = options.dup
-      tsv = Association.database(file, options.merge(:persist => persist))
+      tsv = Association.database(file, options.merge(:persist => persist, :unnamed => true))
       tsv = tsv.to_double unless tsv.type == :double
 
       tsv.annotate data

data/lib/rbbt/knowledge_base/traverse.rb

@@ -46,11 +46,12 @@ class KnowledgeBase
       assignments[target] = (matches.any? ? matches.target.uniq : []) if is_wildcard? target
     end
 
-    def find_paths(rules, all_matches, assignments)
+    def clean_matches(rules, all_matches, assignments)
       paths = {}
 
       rules.zip(all_matches).each do |rule, matches|
         source, db, target = rule.split /\s+/
+
         if is_wildcard? source
           assigned = assignments[source]
           matches = matches.select{|m| assigned.include? m.source }
@@ -63,11 +64,78 @@ class KnowledgeBase
 
         paths[rule] = matches
       end
+
       paths
     end
 
+    def _fp(rules, clean_matches, assignments)
+      return true if rules.empty?
+
+      rule, *rest = rules
+      source, db, target = rule.split /\s+/
+
+      paths = {}
+      matches = clean_matches[rule]
+      Annotated.purge(matches).each do |match|
+        new_assignments = nil
+        match_source, _sep, match_target = match.partition "~"
+
+        if is_wildcard? source
+          next if assignments[source] and assignments[source]  != match_source
+          new_assignments ||= assignments.dup
+          new_assignments[source] = match_source
+        end
+
+        if is_wildcard? target
+          next if assignments[target] and assignments[target]  != match_target
+          new_assignments ||= assignments.dup
+          new_assignments[target] = match_target
+        end
+
+        new_paths = _fp(rest, clean_matches, new_assignments)
+        next unless new_paths
+        paths[match] = new_paths
+      end
+
+      return false if paths.empty?
+
+      paths 
+    end
+
+    def _ep(paths)
+      found = []
+      paths.each do |match,_next|
+        case _next
+        when TrueClass
+          found << [match]
+        when FalseClass
+          next
+        else
+          _ep(_next).each do |_n|
+            found << [match] + _n
+          end
+        end
+      end
+      found
+    end
+
+    def find_paths(rules, all_matches, assignments)
+      clean_matches = clean_matches(rules, all_matches, assignments)
+
+      path_hash = _fp(rules, clean_matches, {})
+
+      return [] unless path_hash
+      _ep(path_hash).collect do |path|
+        path.zip(clean_matches.values_at(*rules)).collect do |item, matches|
+          matches.first.annotate item.dup
+        end
+      end
+    end
+
+
     def traverse
       all_matches = []
+
       rules.each do |rule|
         rule = rule.strip
         next if rule.empty?
@@ -76,6 +144,7 @@ class KnowledgeBase
         source_entities, target_entities = identify db, source, target
 
         matches = kb.subset(db, :source => source_entities, :target => target_entities)
+
         if conditions
           conditions.split(/\s+/).each do |condition|
             if condition.index "="
@@ -88,6 +157,7 @@ class KnowledgeBase
         end
 
         reassign matches, source, target
+
         all_matches << matches
       end
 

data/lib/rbbt/persist.rb

@@ -72,7 +72,7 @@ module Persist
     Path.setup(persistence_dir) unless Path === persistence_dir
 
     filename = perfile.gsub(/\s/,'_').gsub(/\//,'>')
-    clean_options = options
+    clean_options = options.dup
     clean_options.delete :unnamed
     clean_options.delete "unnamed"
 

data/lib/rbbt/tsv/accessor.rb

@@ -252,9 +252,16 @@ module TSV
       if self.include? key
         new = []
         self[key, true].each_with_index do |v,i|
-          new << (v << values[i])
+          _v = values[i]
+          case _v
+          when Array
+            _n = v + _v
+          else
+            _n = v << _v
+          end
+          new << _n
         end
-        self[key] == new
+        self[key] = new
       else
         self[key] = Array === values.first ? values.dup : values.collect{|v| [v] }
       end

data/lib/rbbt/tsv/manipulate.rb

@@ -284,6 +284,8 @@ module TSV
 
       data.extend TSV unless TSV === data
       self.annotate(data)
+      data.entity_options = self.entity_options
+      data.entity_templates = self.entity_templates
 
       data.key_field = new_key_field_name
       data.fields = new_field_names

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

@@ -535,9 +535,6 @@ module TSV
     bar = Misc.process_options options, :bar
     bar ||= Misc.process_options options, :progress
     options[:bar] = case bar
-                    when Step
-                      max = guess_max(obj)
-                      Log::ProgressBar.new_bar(max, {:desc => bar.status, :file => bar.file(:progress)}) 
                     when String
                       max = guess_max(obj)
                       Log::ProgressBar.new_bar(max, {:desc => bar}) 
@@ -554,7 +551,12 @@ module TSV
                       bar.max ||= guess_max(obj)
                       bar
                     else
-                      bar
+                      if (defined? Step and Step === bar)
+                        max = guess_max(obj)
+                        Log::ProgressBar.new_bar(max, {:desc => bar.status, :file => bar.file(:progress)}) 
+                      else
+                        bar
+                      end
                     end
 
     if into

data/lib/rbbt/tsv/parser.rb

@@ -284,6 +284,8 @@ module TSV
 
     def cast_values_single(value)
       case
+      when (value.nil? or value.empty?)
+        nil
       when Symbol === cast
         value.send(cast)
       when Proc === cast
@@ -294,27 +296,27 @@ module TSV
     def cast_values_list(values)
       case
       when Symbol === cast
-        values.collect{|v| v.send(cast)}
+        values.collect{|v| v.nil? or v.empty? ? nil : v.send(cast)}
       when Proc === cast
-        values.collect{|v| cast.call v}
+        values.collect{|v| v.nil? or v.empty? ? nil : cast.call(v)}
       end
     end
 
     def cast_values_flat(values)
       case
       when Symbol === cast
-        values.collect{|v| v.send(cast)}
+        values.collect{|v| v.nil? or v.empty? ? nil : v.send(cast)}
       when Proc === cast
-        values.collect{|v| cast.call v }
+        values.collect{|v| v.nil? or v.empty? ? nil : cast.call(v) }
       end
     end
 
     def cast_values_double(values)
       case
       when Symbol === cast
-        values.collect{|list| list.collect{|v| v.send(cast)}}
+        values.collect{|list| list.collect{|v| v.nil? or v.empty? ? nil : v.send(cast)}}
       when Proc === cast
-        values.collect{|list| list.collect{|v| cast.call v }}
+        values.collect{|list| list.collect{|v| v.nil? or v.empty? ? nil : cast.call(v) }}
       end
     end
 
@@ -539,7 +541,7 @@ module TSV
           desc = monitor[:desc] if monitor.include? :desc 
           step = monitor[:step] if monitor.include? :step 
         end
-        progress_monitor = Log::ProgressBar.new(size, :desc => desc)
+        progress_monitor = Log::ProgressBar.new_bar(size, :desc => desc)
       end
 
       # parser 
@@ -548,8 +550,9 @@ module TSV
 
         while not line.nil? 
           begin
-            #progress_monitor.tick(stream.pos) if progress_monitor 
-            progress_monitor.tick if progress_monitor 
+            if progress_monitor
+              progress_monitor.tick(line.bytesize)
+            end
 
             raise SKIP_LINE if line.empty?
 
@@ -588,6 +591,7 @@ module TSV
           end
         end
       ensure
+        Log::ProgressBar.remove_bar(progress_monitor)
         stream.close unless stream.closed?
         stream.join if stream.respond_to? :join and not stream.joined?
       end

data/lib/rbbt/util/R.rb

@@ -8,13 +8,20 @@ module R
   UTIL    = File.join(LIB_DIR, 'util.R')
   PLOT    = File.join(LIB_DIR, 'plot.R')
 
-  def self.run(command, options = {})
+  def self.run(command, source = nil, options = {})
     cmd =<<-EOF
 # Loading basic rbbt environment
 source('#{UTIL}');
 
     EOF
 
+    require_sources  = source.collect{|source|
+      source = R::LIB_DIR["plot.R"] if source == :plot
+      "source('#{source}')"
+    } * ";\n" if Array === source and source.any?
+
+    cmd << require_sources + "\n\n" if require_sources
+
     case
     when IO === command
       cmd << command.read

data/lib/rbbt/util/log/progress.rb

@@ -16,7 +16,7 @@ module Log
       @last_count = nil
       @last_percent = nil
       @depth = depth
-      @desc = desc
+      @desc = desc.nil? ? nil : desc.gsub(/\n/,' ')
       @file = file
     end
 
@@ -24,9 +24,9 @@ module Log
       (@ticks * 100) / @max
     end
 
-    def tick(step = nil)
+    def tick(step = 1)
       return if ENV["RBBT_NO_PROGRESS"] == "true"
-      @ticks += 1
+      @ticks += step
 
       begin
         time = Time.now

data/lib/rbbt/workflow.rb

@@ -41,7 +41,12 @@ module Workflow
 
   def self.load_workflow_file(filename)
     begin
-      $LOAD_PATH.unshift(File.join(File.dirname(File.expand_path(filename)), 'lib'))
+      workflow_lib_dir = File.join(File.dirname(File.expand_path(filename)), 'lib')
+      #$LOAD_PATH.unshift(File.join(File.dirname(File.expand_path(filename)), 'lib'))
+      if File.directory? workflow_lib_dir
+        Log.debug "Adding workflow lib directory to LOAD_PATH: #{workflow_lib_dir}"
+        $LOAD_PATH.unshift(workflow_lib_dir)
+      end
 
       filename = File.expand_path(filename)
 

data/test/rbbt/knowledge_base/test_traverse.rb

@@ -8,12 +8,34 @@ class TestKnowledgeBaseTraverse < Test::Unit::TestCase
     Genomics.knowledge_base
   end
 
-  def test_traverse
+  def _test_traverse
     rules = []
-    rules << "SF3B1 pina ?1 - Method=MI:0006"
-    rules << "TP53 pina ?1"
+    rules << "?1 pina SF3B1 - Method=MI:0006"
+    rules << "TP53 pina ?2"
+    rules << "?2 pina ?1"
     res =  kb.traverse rules
+    iii res
     assert res.first.include? "?1"
   end
+
+  def _test_path
+    rules = []
+    rules << "?1 pina ARPC2"
+    rules << "ARPC3 pina ?2"
+    rules << "?2 pina ?1"
+    res =  kb.traverse rules
+    assert res.first.include? "?1"
+    iii res.last.first
+  end
+
+  def test_path2
+    rules = []
+    rules << "?1 pina SF3B1"
+    rules << "?2 pina SF3B1"
+    rules << "?1 pina ?2"
+    res =  kb.traverse rules
+    assert res.first.include? "?1"
+    iii res.last.first.first.source
+  end
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.0
+  version: 5.17.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-02-20 00:00:00.000000000 Z
+date: 2015-03-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake