rbbt-util 5.27.1 → 5.27.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 9692dd68f20cec3b8688cc9d75e1bcd4d75a024924c56c191a87897162d34ef4
+  metadata.gz: 258aa01482866ef7b940790ad6f10d077a0cd721b972cbb939412c3691595acc
+  data.tar.gz: 9adb68a2c9ddfa77a3be419dd106e4083e11933dd6653b4d6e0bfa921edab187
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+  metadata.gz: 4df9dcbc8280023faa1e6c2e6a9393a9ae66e4513a95cdeae94256f5fc61f0e6691e114cd1d40a900041e1769988b2a69751f282fc95c0c134acb44cac3ed40c
+  data.tar.gz: b72bd064835be7c5dcfcf180ff87d6e22fced3f8833d9479f607ab64760594c7d7d25d84cd828b33f0a7d72208983b8c89e26d8924e91afc81ba5e5943ef462d

data/lib/rbbt/annotations/util.rb

@@ -145,10 +145,9 @@ module Annotated
 
              end
 
-    fields = fields.collect{|f| f.to_s}
+    fields = fields.collect{|f| f.to_s}.uniq
 
     case
-
     when (Annotated === annotations and not (AnnotatedArray === annotations and annotations.double_array))
       tsv = TSV.setup({}, :key_field => "List", :fields => fields, :type => :list, :unnamed => true)
 

data/lib/rbbt/entity.rb

@@ -194,13 +194,16 @@ module Entity
           multi_name = "_multiple_" << name
 
           define_method multi_name do
-            if self.instance_variable_get("@multiple_result")
-              return self.instance_variable_get("@multiple_result")
+            if self.instance_variable_get("@multiple_result_" + name.to_s)
+              return self.instance_variable_get("@multiple_result_" + name.to_s)
             end
-            raise MultipleEntity, "Entity #{name} runs with multiple entities: #{self}"
+            raise MultipleEntity, "Entity #{name} runs with multiple entities"
           end
 
           define_method name do |*args|
+            if self.instance_variable_get("@multiple_result_" + name.to_s)
+              return self.instance_variable_get("@multiple_result_" + name.to_s)
+            end
             obj = if Array === self
                     self
                   elsif self.respond_to?(:container) && Array === self.container
@@ -222,11 +225,11 @@ module Entity
             case res
             when Array
               missing.zip(res).each do |o,res|
-                o.instance_variable_set("@multiple_result", res)
+                o.instance_variable_set("@multiple_result_" + name.to_s, res)
               end
             when Hash
               res.each do |o,res|
-                o.instance_variable_set("@multiple_result", res)
+                o.instance_variable_set("@multiple_result_" + name.to_s, res)
               end
             end
 

data/lib/rbbt/knowledge_base/entity.rb

@@ -5,14 +5,15 @@ class KnowledgeBase
 
   def select_entities(name, entities, options = {})
     index = get_index(name, options)
+
     source_field = index.source_field
     target_field = index.target_field
 
     source_type = Entity.formats[source_field] 
     target_type = Entity.formats[target_field]
 
-    source_entities = entities[:source] || entities[source_field] || entities[Entity.formats[source_field].to_s] 
-    target_entities = entities[:target] || entities[target_field] || entities[Entity.formats[target_field].to_s]
+    source_entities = entities[:source] || entities[source_field] || entities[Entity.formats[source_field].to_s] || entities[:both]
+    target_entities = entities[:target] || entities[target_field] || entities[Entity.formats[target_field].to_s] || entities[:both]
 
     [source_entities, target_entities]
   end

data/lib/rbbt/knowledge_base/query.rb

@@ -10,6 +10,7 @@ class KnowledgeBase
 
   def subset(name, entities, options = {}, &block)
     entities, options = options, entities if entities.nil? and Hash === options
+
     entities = case entities
                when :all
                  {:target => :all, :source => :all}
@@ -23,7 +24,15 @@ class KnowledgeBase
                  raise "Entities are not a Hash or an AnnotatedArray: #{Misc.fingerprint entities}"
                end
 
+    identify, identify_source, identify_target = entities.merge(options || {}).values_at :identify, :identify_source, :identify_target
+
     source, target = select_entities(name, entities, options)
+    
+    source = identify_source(name, source) if identify_source
+    target = identify_target(name, target) if identify_target
+
+    source = identify(name, source) if identify && !identify_source
+    target = identify(name, target) if identify && !identify_target
 
     return [] if source.nil? or target.nil?
     return [] if Array === target and target.empty?

data/lib/rbbt/persist.rb

@@ -407,7 +407,6 @@ module Persist
           repo.read_and_close do
             keys = repo.range subkey + 0.chr, true, subkey + 254.chr, true
           end
-          repo.close
         else
           repo.read_and_close do
             keys = repo.range subkey + 0.chr, true, subkey + 254.chr, true
@@ -461,13 +460,13 @@ module Persist
               entities.each_with_index do |e,i|
                 next if e.nil?
                 tsv_values = e.tsv_values("literal", "annotation_types", "JSON") 
-                repo[subkey + e.id << ":ANNOTATED_DOUBLE_ARRAY:" << i.to_s] = tsv_values
+                repo[subkey + "ANNOTATED_DOUBLE_ARRAY:" << i.to_s] = tsv_values
               end
             else
               entities.each_with_index do |e,i|
                 next if e.nil?
                 tsv_values = e.tsv_values("literal", "annotation_types", "JSON") 
-                repo[subkey + e.id << ":" << i.to_s] = tsv_values
+                repo[subkey + i.to_s] = tsv_values
               end
             end
           end

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

@@ -33,7 +33,29 @@ module Persist
     end
 
     def read?
-      ! write?
+      ! (write? || closed?)
+    end
+
+    def write(*args)
+      begin
+        super(*args)
+        @writable = true
+      rescue NoMethodError
+      end
+    end
+
+    def close(*args)
+      begin
+        super(*args)
+      rescue NoMethodError
+      end
+    end
+
+    def read(*args)
+      begin
+        super(*args)
+      rescue NoMethodError
+      end
     end
 
     def collect
@@ -53,16 +75,27 @@ module Persist
     end
 
     def lock
+      #return yield if @locked
       lock_filename = Persist.persistence_path(persistence_path, {:dir => TSV.lock_dir})
       Misc.lock(lock_filename) do
-        yield
+        begin
+          @locked = true
+          yield
+        ensure
+          @locked = false
+        end
       end
     end
 
     def write_and_read
-      #lock_filename = Persist.persistence_path(persistence_path, {:dir => TSV.lock_dir})
-      #mutex.synchronize do
-      #Misc.lock(lock_filename) do
+      if write?
+        begin
+          return yield
+        ensure
+          read
+        end
+      end
+
       lock do
         write true if closed? or not write?
         begin
@@ -71,14 +104,17 @@ module Persist
           read
         end
       end
-      #end
-      #end
     end
 
     def write_and_close
-      #lock_filename = Persist.persistence_path(persistence_path + '.write', {:dir => TSV.lock_dir})
-      #mutex.synchronize do
-      #Misc.lock(lock_filename, true) do
+      if write?
+        begin
+          return yield
+        ensure
+          close
+        end
+      end
+
       lock do
         write true if closed? || ! write?
         res = begin
@@ -91,11 +127,17 @@ module Persist
               end
         res
       end
-      #end
-      #end
     end
 
     def read_and_close
+      if read?
+        begin
+          return yield
+        ensure
+          close
+        end
+      end
+
       lock do
         read true if closed? || ! read?
         begin

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

@@ -374,7 +374,7 @@ module TSV
       when (defined? Step and Step)
 
         obj.clean if obj.aborted? or obj.recoverable_error?
-        obj.run(true) unless obj.done? or obj.started?
+        obj.run(true) unless obj.done? || obj.started? || obj.result
 
         stream = obj.get_stream
 

data/lib/rbbt/tsv/util.rb

@@ -122,6 +122,7 @@ module TSV
         end
       else
         file.grace
+
         stream = file.get_stream
         if stream && ! stream.closed?
           stream

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

@@ -108,7 +108,7 @@ class Step
       @result = self._exec
       @result = @result.stream if TSV::Dumper === @result
     end
-    (no_load or ENV["RBBT_NO_STREAM"]) ? @result : prepare_result(@result, @task.result_description)
+    (no_load || ENV["RBBT_NO_STREAM"]) ? @result : prepare_result(@result, @task.result_description)
   end
 
   def updatable?

data/lib/rbbt/workflow/usage.rb

@@ -71,7 +71,7 @@ module Workflow
     @dep_tree ||= {}
     @dep_tree[name] ||= begin
                         dep_tree = {}
-                        self.task_dependencies[name].reverse.each do |dep|
+                        self.task_dependencies[name.to_sym].reverse.each do |dep|
                           dep = dep.first if Array === dep && dep.length == 1
                           dep = dep.dependency if DependencyBlock === dep
 
@@ -88,23 +88,38 @@ module Workflow
                           key = [workflow, task]
 
                           dep_tree[key] = workflow.dep_tree(task)
-                        end
+                        end if self.task_dependencies[name.to_sym]
                         dep_tree
                       end
   end
 
+  def _prov_tasks(tree)
+    tasks = [] 
+    heap = [tree]
+    while heap.any?
+      t = heap.pop
+      t.each do |k,v|
+        tasks << k
+        heap << v
+      end
+    end
+    tasks
+  end
+
   def prov_string(tree)
     description = ""
 
     last = nil
     seen = Set.new
-    tree.collect.to_a.flatten.select{|e| Symbol === e }.each do |task_name|
 
-      child = last && last.include?(task_name)
-      first = last.nil?
-      last = dep_tree(task_name).collect.to_a.flatten.select{|e| Symbol === e}
+    tasks = _prov_tasks(tree)
+    tasks.each do |workflow,task_name|
+
+      next if seen.include?([workflow,task_name])
 
-      next if seen.include?(task_name)
+      child = last && last.include?([workflow, task_name])
+      first = last.nil?
+      last = _prov_tasks(workflow.dep_tree(task_name))
 
       if child
         description << "->" << task_name.to_s
@@ -113,6 +128,8 @@ module Workflow
       else
         description << ";" << task_name.to_s
       end
+      
+      seen << [workflow, task_name]
     end
     description
   end
@@ -177,7 +194,7 @@ module Workflow
         description = task.description || ""
         description = description.split("\n\n").first
 
-        next if abridge and ! final.include?(name)
+        next if abridge && ! final.include?(name)
         puts Misc.format_definition_list_item(name.to_s, description, Log.terminal_width, 20, :yellow)
 
         prov_string = prov_string(dep_tree(name))

data/share/install/software/lib/install_helpers

@@ -203,6 +203,8 @@ prepare_make(){
     local old_pwd="`expand_path $(pwd)`"
     cd "`build_dir`"
 
+    [ -f bootstrap ] && (./bootstrap || exit -1)
+
     [ -d src -a ! -e CMakeLists.txt -a ! -e Makefile -a ! -e configure ] && cd src
 
     if [ -f config/m4 ]; then

data/share/rbbt_commands/tsv/get

@@ -47,6 +47,28 @@ fields = options[:fields]
 key_field = options[:key_field]
 fields = fields.split(/[,|]/, -1) unless fields.nil?
 
+if TSV === tsv
+  v = tsv[key]
+  fields ||= tsv.fields
+  puts Log.color(:blue, "Key: #{ key }")
+  if fields
+    if fields.length == 1
+      if options[:lines]
+        puts (Array === v ? v.flatten*"\n" : v.to_s ) 
+      else
+        puts (Array === v ? v.flatten*"\t" : v.to_s ) 
+      end
+    else
+      fields.zip(v).each do |field,v|
+        puts "#{Log.color :magenta, field+":"} #{v}"
+      end
+    end
+  else
+    puts "#{Log.color :magenta, "value:"} #{v}"
+  end
+  exit
+end
+
 parser = TSV::Parser.new tsv, :key_field => key_field,  :fields => fields, :type => options[:type], :header_hash => options[:header_hash], :sep => options[:sep]
 fields ||= parser.fields
 
@@ -54,15 +76,19 @@ TSV.traverse(parser) do |k,v|
   next unless k.include? key
   k = k.first if Array === k
   puts Log.color(:blue, "Key: #{ k }")
-  if fields.length == 1
-    if options[:lines]
-      puts (Array === v ? v.flatten*"\n" : v.to_s ) 
+  if fields
+    if fields.length == 1
+      if options[:lines]
+        puts (Array === v ? v.flatten*"\n" : v.to_s ) 
+      else
+        puts (Array === v ? v.flatten*"\t" : v.to_s ) 
+      end
     else
-      puts (Array === v ? v.flatten*"\t" : v.to_s ) 
+      fields.zip(v).each do |field,v|
+        puts "#{Log.color :magenta, field+":"} #{v}"
+      end
     end
   else
-    fields.zip(v).each do |field,v|
-      puts "#{Log.color :magenta, field+":"} #{v}"
-    end
+    puts "#{Log.color :magenta, "value:"} #{Misc.fingerprint v}"
   end
 end

data/share/rbbt_commands/workflow/task

@@ -416,7 +416,7 @@ begin
 
     job.fork
   else
-    job.produce
+    job.run(:stream)
     res = job
   end
 

data/test/rbbt/knowledge_base/test_query.rb

@@ -24,7 +24,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
 
   EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup 
 
-  KNOWLEDGE_BASE = KnowledgeBase.new '/tmp/kb.foo2', "Hsa"
+  KNOWLEDGE_BASE = KnowledgeBase.new Rbbt.tmp.test.kb_foo2, "Hsa"
   KNOWLEDGE_BASE.format = {"Gene" => "Ensembl Gene ID"}
 
   KNOWLEDGE_BASE.register :effects, EFFECT_TSV, EFFECT_OPTIONS.dup

data/test/rbbt/test_entity.rb

@@ -71,7 +71,9 @@ module ReversableString
       }
     end
   end
+
   persist :multiple_annotation_list, :annotations, :dir => TmpFile.tmp_file
+  #persist :multiple_annotation_list, :annotations, :dir => Rbbt.tmp.test.annots
 end
 
 class TestEntity < Test::Unit::TestCase
@@ -195,33 +197,40 @@ class TestEntity < Test::Unit::TestCase
     string3 = 'AAABBBCCC_3'
     string4 = 'AAABBBCCC_4'
 
+
+    $processed_multiple = []
+    Log.severity = 0
+
     array = ReversableString.setup([string1, string2])
     assert_equal [string1, string2].collect{|s| s.chars}, array.multiple_annotation_list
-
     assert_equal string1.length, array[0].multiple_annotation_list.length
     assert_equal $processed_multiple, [string1, string2]
 
     array = ReversableString.setup([string2, string3])
-    assert_equal string2.length, array[0].multiple_annotation_list.length
+    assert_equal [string2, string3].collect{|s| s.chars}, array.multiple_annotation_list
+    assert_equal string3, array.multiple_annotation_list.last * ""
     assert_equal $processed_multiple, [string1, string2, string3]
 
+    $processed_multiple = []
     array = ReversableString.setup([string2, string3])
+    assert_equal [string2, string3].collect{|s| s.chars}, array.multiple_annotation_list
     assert_equal string2.length, array[0].multiple_annotation_list.length
-    assert_equal $processed_multiple, [string1, string2, string3]
+    assert_equal $processed_multiple, []
 
     $processed_multiple = []
     array = ReversableString.setup([string2, string3, string4])
-    assert_equal string2.length, array[0].multiple_annotation_list.length
+    assert_equal string2.length, array.multiple_annotation_list[0].length
     assert_equal $processed_multiple, [string4]
 
     string1 = 'aaabbbccc'
     string2 = 'AAABBBCCC'
     string3 = 'AAABBBCCC_3'
     string4 = 'AAABBBCCC_4'
+
     $processed_multiple = []
     array = ReversableString.setup([string2, string3, string4])
     assert_equal string2.length, array[0].multiple_annotation_list.length
-    assert_equal $processed_multiple, [string4]
+    assert_equal $processed_multiple, []
 
   end
 

data/test/rbbt/test_knowledge_base.rb

@@ -92,9 +92,9 @@ class TestKnowledgeBase < Test::Unit::TestCase
       assert downstream.length < downstream.follow(kb, :tfacts,false).flatten.length
 
       Misc.benchmark(50) do
-        downstream.follow(kb, :tfacts,false)
-        downstream.backtrack(kb, :tfacts,false)
-        downstream.expand(kb, :tfacts,false)
+        downstream.follow(kb, :tfacts, false)
+        downstream.backtrack(kb, :tfacts, false)
+        downstream.expand(kb, :tfacts, false)
       end
 
       Misc.benchmark(50) do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.27.1
+  version: 5.27.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-04-19 00:00:00.000000000 Z
+date: 2020-04-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake