rbbt-util 5.19.9 → 5.19.10

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 948a27e4e5063aa205ff63017423494b6d5cec7e
+  metadata.gz: a2ef5af815d45af2cfaaa690e733714b5352fd2a
+  data.tar.gz: ba78cb831ba748606f3b75b36fc9292cd98d6ddb
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+  metadata.gz: 2abbf6a68b9bb7721e924025d2f51e0174ecdee38cdb132fee51dbb0eb20449eae4e106b783e7b015e157d537e34482d7207a2d9b5871caf5c345d63f578ec28
+  data.tar.gz: d6b7cd2954c7f4cc5f4796c7b677beb1c82e178e430dac066d3d4db9e99d56e9b1f1fecc4440e69ed1c08dc9e00e028aaeb07ffff4f28735d4a791b65fa9b935

data/lib/rbbt/association/database.rb

@@ -34,6 +34,7 @@ module Association
       Log.debug("Changing source format from #{tsv.key_field} to #{source_final_format}")
 
       identifier_files = tsv.identifier_files.dup
+      identifier_files = [Organism.identifiers("NAMESPACE")] if identifier_files.empty?
       identifier_files.concat Entity.identifier_files(source_final_format) if defined? Entity
       identifier_files.uniq!
       identifier_files.collect!{|f| f.annotate(f.gsub(/\bNAMESPACE\b/, namespace))} if namespace

data/lib/rbbt/association/util.rb

@@ -42,7 +42,7 @@ module Association
   end
 
   def self.extract_specs(all_fields=nil, options = {})
-    source, source_format, target, target_format = Misc.process_options options, :source, :source_format, :target, :target_format
+    source, source_format, target, target_format, format = Misc.process_options options, :source, :source_format, :target, :target_format, :format
 
     key_field, *fields = all_fields.nil? ? [nil] : all_fields
 
@@ -84,6 +84,19 @@ module Association
       end
     end
 
+    # If format is specified, then perhaps we need to change the
+    if target_specs[2].nil? 
+      target_type = Entity.formats[target_specs[1] || target_specs[0]]
+      target_specs[2] = format[target_type.to_s] if format
+      target_specs[2] = nil if target_specs[2] == target_specs[0] or target_specs[2] == target_specs[1]
+    end
+
+    if source_specs[2].nil? 
+      source_type = Entity.formats[source_specs[1] || source_specs[0]]
+      source_specs[2] = format[source_type.to_s] if format
+      source_specs[2] = nil if source_specs[2] == source_specs[0] or source_specs[2] == source_specs[1]
+    end
+
     {:source => source_specs, :target => target_specs}
   end
 

data/lib/rbbt/knowledge_base/registry.rb

@@ -43,8 +43,8 @@ class KnowledgeBase
     options[:organism] ||= options[:namespace] ||= self.namespace
     @indices[[name, options]] ||= 
       begin 
-        fp = Misc.fingerprint([name,options])
-        key = name.to_s + "_" + Misc.digest(fp)
+        fp = Misc.hash2md5(options)
+        key = name.to_s + "_" + fp
 
         Persist.memory("Index:" << [key, dir] * "@") do
           options = options.dup
@@ -67,7 +67,7 @@ class KnowledgeBase
 
           index = if persist_file.exists? and persist_options[:persist] and not persist_options[:update]
                     Log.low "Re-opening index #{ name } from #{ Misc.fingerprint persist_file }. #{options}"
-                    Association.index(nil, options, persist_options.dup)
+                    Association.index(file, options, persist_options.dup)
                   else
                     options = Misc.add_defaults options, registered_options if registered_options
                     raise "Repo #{ name } not found and not registered" if file.nil?
@@ -110,7 +110,7 @@ class KnowledgeBase
 
           database = if persist_file.exists? and persist_options[:persist] and not persist_options[:update]
                     Log.low "Re-opening database #{ name } from #{ Misc.fingerprint persist_file }. #{options}"
-                    Association.open(nil, options, persist_options)
+                    Association.open(file, options, persist_options)
                   else
                     options = Misc.add_defaults options, registered_options if registered_options
                     raise "Repo #{ name } not found and not registered" if file.nil?

data/lib/rbbt/persist.rb

@@ -431,7 +431,8 @@ module Persist
         end
 
       else
-        persist_file(path.find, type, persist_options, &block)
+        path = path.find if Path === path
+        persist_file(path, type, persist_options, &block)
       end
 
     end

data/share/rbbt_commands/workflow/knowledge_base

@@ -13,7 +13,6 @@ $ rbbt workflow knowledge_base <workflow> [<database>] [<action>] [<options>]
 Access workflow knowledge base
 
 -h--help Show this help:
--cl--clean Clean the last step of the job so that it gets recomputed:
 -s--source_entities* Source entities
 -sf--source_format* Source format
 -t--target_entities* Target entities

data/test/rbbt/tsv/test_manipulate.rb

@@ -20,7 +20,7 @@ rowa    a|aa    b|BB  C|CC
   end
 
 
-  def _test_through
+  def test_through
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -39,7 +39,7 @@ row3    a    C    Id4
     end
   end
 
-  def _test_reorder_simple
+  def test_reorder_simple
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -61,7 +61,7 @@ row3    a    C    Id4
     end
   end
 
-  def _test_reorder_remove_field
+  def test_reorder_remove_field
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -83,7 +83,7 @@ row3    a    C    Id4
     end
   end
 
-  def _test_slice
+  def test_slice
     content =<<-EOF
 #ID ValueA ValueB Comment
 row1 a b c
@@ -96,7 +96,7 @@ row2 A B C
     end
   end
 
-  def _test_select
+  def test_select
      content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -134,7 +134,7 @@ row3    a    C    Id4
     end
   end
 
-  def _test_select_invert
+  def test_select_invert
      content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -165,7 +165,7 @@ row3    a    C    Id4
     end
   end
 
-  def _test_process
+  def test_process
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -184,7 +184,7 @@ row3    a    C    Id4
     end
   end
 
-  def _test_add_field
+  def test_add_field
      content =<<-EOF
 #Id    LetterValue:ValueA    LetterValue:ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -202,7 +202,7 @@ row3    a    C    Id4
     end
   end
 
-  def _test_add_field_double_with_list_result
+  def test_add_field_double_with_list_result
      content =<<-EOF
 #Id    LetterValue:ValueA    LetterValue:ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -221,7 +221,7 @@ row3    a    C    Id4
     end
   end
 
-  def _test_through_headless
+  def test_through_headless
      content =<<-EOF
 row1    a|aa|aaa    b    Id1|Id2
 row2    A    B    Id3
@@ -231,17 +231,17 @@ row3    a    C    Id4
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(filename, :sep => /\s+/)
 
-      _test = false
+      test = false
       tsv.through do
-        _test = true
+        test = true
       end
-      assert _test
+      assert test
 
     end
  
   end
 
-  def _test_reorder_flat
+  def test_reorder_flat
     content =<<-EOF
 #Id    ValueA    
 row1    a aa aaa
@@ -257,7 +257,7 @@ row3    a
     end
   end
 
-  def _test_transpose
+  def test_transpose
      content =<<-EOF
 #: :type=:list
 #Row   vA   vB   vID
@@ -275,7 +275,7 @@ row3    a    C    Id4
  
   end
 
-  def _test_through_flat
+  def test_through_flat
      content =<<-EOF
 #: :type=:flat
 #Row   vA

data/test/rbbt/util/R/test_model.rb

@@ -124,7 +124,6 @@ data = rbbt.model.inpute(data, CI ~ Dose, method=drm, classes='numeric', fct=LL.
     y = 10 + 3 * x 
 
     pred = model.predict x
-    iii model.predict_interval(x)
     assert pred > y and pred < y + 4
   end
 end

data/test/rbbt/workflow/test_step.rb

@@ -141,9 +141,10 @@ class TestStep < Test::Unit::TestCase
       end
       TmpFile.with_file do |tmp|
         step = Step.new tmp, task
-        job = step.fork
-        while not job.done? do sleep 1 end
-        assert_equal "TEST", Open.read(job.file("test"))
+        #job = step.fork
+        #while not job.done? do sleep 1 end
+        step.run
+        assert_equal "TEST", Open.read(step.file("test"))
       end
     end
   end
@@ -153,6 +154,8 @@ class TestStep < Test::Unit::TestCase
       task  = Task.setup do 
         message "WRITE"
         Open.write(file("test"),"TEST")
+        Open.write(path,"done")
+        nil
       end
       
       TmpFile.with_file do |tmp|
@@ -175,10 +178,11 @@ class TestStep < Test::Unit::TestCase
 
       TmpFile.with_file do |tmp|
         step = Step.new File.join(tmp, 'subdir1', 'subdir2'), task
-        job = step.fork
-        while not job.done? do sleep 1 end
-        assert_equal "TEST", Open.read(job.file("test"))
-        assert job.messages.include? "WRITE"
+        #job = step.fork
+        #while not job.done? do sleep 1 end
+        step.run
+        assert_equal "TEST", Open.read(step.file("test"))
+        assert step.messages.include? "WRITE"
       end
     end
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.19.9
+  version: 5.19.10
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-12-17 00:00:00.000000000 Z
+date: 2016-01-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake