rbbt-util 5.19.10 → 5.19.11

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: a2ef5af815d45af2cfaaa690e733714b5352fd2a
-  data.tar.gz: ba78cb831ba748606f3b75b36fc9292cd98d6ddb
+  metadata.gz: d033f774277a3c6644e82ccb1d904d394dd68fe8
+  data.tar.gz: 654e1dabdcabf1bd94d5ad4bc48f1284ffc26007
 SHA512:
-  metadata.gz: 2abbf6a68b9bb7721e924025d2f51e0174ecdee38cdb132fee51dbb0eb20449eae4e106b783e7b015e157d537e34482d7207a2d9b5871caf5c345d63f578ec28
-  data.tar.gz: d6b7cd2954c7f4cc5f4796c7b677beb1c82e178e430dac066d3d4db9e99d56e9b1f1fecc4440e69ed1c08dc9e00e028aaeb07ffff4f28735d4a791b65fa9b935
+  metadata.gz: 9595ff8109bcdaac80a1e2f04eb4516814586de65605a4721ece5f9754d8dcdec31176db1933bf397c2c16d6b99bd66c3c4d638a1c722f45a07b55ea412d2ef5
+  data.tar.gz: 7c7d186eedf2bf54debecde2057523fb433c7c9c6fcd12fc46a15f14298c614cc497b569b7d40870f3ecda8081b01a1b2948b62e56f59370b921964df48812c5

data/etc/app.d/knowledge_bases.rb

@@ -0,0 +1,13 @@
+#{{{ Require files
+Rbbt.etc.knowledge_bases.read.split("\n").each do |workflow|
+  next if workflow.empty?
+  Log.debug("syndicating knowledgebase from workflow #{ workflow }")
+  begin
+    wf = Kernel.const_get workflow
+    begin require "rbbt/knowledge_base/#{ workflow }" rescue Exception end
+    KnowledgeBaseRESTHelpers.add_syndication Misc.snake_case(workflow), wf.knowledge_base
+  rescue Exception
+    Log.warn "Exception loading knowledgebase from #{ workflow }"
+    Log.exception $!
+  end
+end if Rbbt.etc.knowledge_bases.exists?

data/lib/rbbt/association/open.rb

@@ -16,9 +16,10 @@ module Association
     persist = persist_options[:persist]
 
     file = version_file(file, options[:namespace]) if options[:namespace] and String === file
-    file = file.call if Proc === file
 
     data = Persist.persist_tsv(file, "Association Database", options, persist_options) do |data|
+      file = file.call if Proc === file
+
       options = options.dup
       tsv = Association.database(file, options.merge(:persist => persist, :unnamed => true))
       tsv = tsv.to_double unless tsv.type == :double

data/lib/rbbt/knowledge_base/traverse.rb

@@ -24,10 +24,10 @@ class KnowledgeBase
 
     def identify(db, source, target)
       source_entities = if is_wildcard? source
-                        assignments[source] || :all
-                      else
-                        kb.identify_source db, source
-                      end
+                          assignments[source] || :all
+                        else
+                          kb.identify_source db, source
+                        end
 
       target_entities = if is_wildcard? target
                           assignments[target] || :all
@@ -42,8 +42,8 @@ class KnowledgeBase
     end
     
     def reassign(matches, source, target)
-      assignments[source] = (matches.any? ? matches.source.uniq : []) if is_wildcard? source
-      assignments[target] = (matches.any? ? matches.target.uniq : []) if is_wildcard? target
+      assignments[source] = (matches.any? ? matches.collect{|m|m.partition("~").first}.uniq : nil) if is_wildcard? source
+      assignments[target] = (matches.any? ? matches.collect{|m|m.partition("~").last}.uniq : nil) if is_wildcard? target
     end
 
     def clean_matches(rules, all_matches, assignments)
@@ -53,13 +53,13 @@ class KnowledgeBase
         source, db, target = rule.split /\s+/
 
         if is_wildcard? source
-          assigned = assignments[source]
-          matches = matches.select{|m| assigned.include? m.source }
+          assigned = assignments[source] || []
+          matches = matches.select{|m| assigned.include? m.partition("~").first }
         end
         
         if is_wildcard? target
-          assigned = assignments[target]
-          matches = matches.select{|m| assigned.include? m.target }
+          assigned = assignments[target] || []
+          matches = matches.select{|m| assigned.include? m.partition("~").last }
         end
 
         paths[rule] = matches
@@ -127,9 +127,29 @@ class KnowledgeBase
       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
+          matches.select{|m| m == item}.first
+        end
+      end
+    end
+
+    def traverse_db(db, source, target, conditions)
+      source_entities, target_entities = identify db, source, target
+
+      options = {:source => source_entities, :target => target_entities}
+      matches = kb.subset(db, options)
+
+      if conditions
+        Misc.tokenize(conditions).each do |condition|
+          if condition.index "="
+            key, value = conditions.split("=")
+            matches = matches.select{|m| Misc.match_value(m.info[key.strip], value)}
+          else
+            matches = matches.select{|m| m.info[condition.strip].to_s =~ /\btrue\b/}
+          end
         end
       end
+
+      matches
     end
 
 
@@ -139,32 +159,92 @@ class KnowledgeBase
       rules.each do |rule|
         rule = rule.strip
         next if rule.empty?
-        source, db, target, conditions = rule.match(/([^\s]+)\s+([^\s]+)\s+([^\s]+)(?:\s+-\s+([^\s]+))?/).captures
 
-        source_entities, target_entities = identify db, source, target
+        if m = rule.match(/([^\s]+)\s+([^\s]+)\s+([^\s]+)(?:\s+-\s+([^\s]+))?/)
+
+          source, db, target, conditions = m.captures
+          if db.include? '?'
+            all_dbs = kb.registry.keys
+            _name, _sep, _kb = db.partition("@")
+            case
+            when _kb[0] == '?'
+              dbs = all_dbs.select{|_db| _db.partition("@").first == _name}
+            when _name[0] == '?'
+              dbs = all_dbs.select{|_db| _db.include?("@") ? db.partition("@").last == _kb : true}
+            end
+          else
+            dbs = [db]
+          end
 
-        matches = kb.subset(db, :source => source_entities, :target => target_entities)
+          rule_matches = []
+          dbs.each do |_db|
+            matches = traverse_db(_db, source, target, conditions)
+
+            next if matches.nil? or matches.empty?
+
+            if db.include? '?'
+              _name, _sep, _kb = db.partition("@")
+              case
+              when _kb[0] == '?'
+                assignments[_kb] ||= []
+                assignments[_kb] << _db.partition("@").reject{|p| p.empty?}.last
+              when _name[0] == '?'
+                assignments[_name] ||= []
+                assignments[_name] << _db.partition("@").first
+              end
+            end
 
-        if conditions
-          conditions.split(/\s+/).each do |condition|
-            if condition.index "="
-              key, value = conditions.split("=")
-              matches = matches.select{|m| m.info[key.strip].to_s =~ /\b#{value.strip}\b/}
-            else
-              matches = matches.select{|m| m.info[condition.strip].to_s =~ /\btrue\b/}
+            matches.each do |m|
+              rule_matches << m
             end
           end
-        end
 
-        reassign matches, source, target
+          reassign rule_matches, source, target
 
-        all_matches << matches
+          all_matches << rule_matches
+        else
+          raise "Rule not understood: #{rule}"
+        end
       end
 
       paths = find_paths rules, all_matches, assignments
-      
+
       [assignments, paths]
     end
+
+    #def traverse
+    #  all_matches = []
+
+    #  rules.each do |rule|
+    #    rule = rule.strip
+    #    next if rule.empty?
+    #    source, db, target, conditions = rule.match(/([^\s]+)\s+([^\s]+)\s+([^\s]+)(?:\s+-\s+([^\s]+))?/).captures
+
+    #    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 "="
+    #          key, value = conditions.split("=")
+    #          matches = matches.select{|m| m.info[key.strip].to_s =~ /\b#{value.strip}\b/}
+    #        else
+    #          matches = matches.select{|m| m.info[condition.strip].to_s =~ /\btrue\b/}
+    #        end
+    #      end
+    #    end
+
+    #    reassign matches, source, target
+
+    #    all_matches << matches
+    #  end
+
+    #  paths = find_paths rules, all_matches, assignments
+
+    #  [assignments, paths]
+    #end
+
   end
 
   def traverse(rules)

data/lib/rbbt/util/misc.rb

@@ -20,9 +20,53 @@ require 'rbbt/util/misc/system'
 require 'rbbt/util/misc/objects'
 require 'rbbt/util/misc/manipulation'
 
+require 'to_regexp'
+
 module MultipleResult; end
 
 module Misc
+  def self._convert_match_condition(condition)
+    return true if condition == 'true'
+    return false if condition == 'false'
+    return condition.to_regexp if condition[0] == "/"
+    return [:cmp, $1, $2.to_f] if condition =~ /^([<>]=?)(.*)/
+    return [:invert, _convert_match_condition(condition[1..-1].strip)] if condition[0] == "!"
+    #return {$1 => $2.to_f} if condition =~ /^([<>]=?)(.*)/
+    #return {false => _convert_match_condition(condition[1..-1].strip)} if condition[0] == "!"
+    return condition
+  end
+
+  def self.match_value(value, condition)
+    condition = _convert_match_condition(condition.strip) if String === condition
+
+    case condition
+    when Regexp
+      !! value.match(condition)
+    when NilClass, TrueClass
+      value === TrueClass or (String === value and value.downcase == 'true')
+    when FalseClass
+      value === FalseClass or (String === value and value.downcase == 'false')
+    when String
+      Fixnum === value ? value.to_f == condition.to_f : value == condition
+    when Fixnum
+      value.to_f == condition.to_f
+    when Array
+      case condition.first
+      when :cmp
+        value.to_f.send(condition[1], condition[2])
+      when :invert
+        ! match_value(value, condition[1] )
+      else
+        condition.inject(false){|acc,e| acc = acc ? true : match_value(value, e) }
+      end
+    else
+      raise "Condition not understood: #{Misc.fingerprint condition}"
+    end
+  end
+
+  def self.tokenize(str)
+    str.scan(/"[^"]*"|'[^']*'|[^"'\s]+/)
+  end
 end
 
 module PDF2Text
@@ -36,4 +80,5 @@ module PDF2Text
       CMD.cmd("pdftotext #{pdf_file} -", :pipe => false, :stderr => true)
     end
   end
+
 end

data/lib/rbbt/util/misc/inspect.rb

@@ -207,7 +207,7 @@ module Misc
           when FalseClass
             'false'
           when Hash
-            "{"<< obj.collect{|k,v| obj2str(k) << '=>' << obj2str(v)}*"," << "}"
+            "{"<< obj.collect{|k,v| obj2str(k) + '=>' << obj2str(v)}*"," << "}"
           when Symbol
             obj.to_s
           when String

data/share/config.ru

@@ -40,6 +40,9 @@ app_eval app, Rbbt.etc['app.d/base.rb'].find
 #{{{ RESOURCES
 load_file Rbbt.etc['app.d/resources.rb'].find
 
+#{{{ KNOWLEDGEBASE
+load_file Rbbt.etc['app.d/knowledge_bases.rb'].find
+
 #{{{ ENTITIES
 load_file Rbbt.etc['app.d/entities.rb'].find
 

data/test/rbbt/knowledge_base/test_traverse.rb

@@ -8,24 +8,22 @@ class TestKnowledgeBaseTraverse < Test::Unit::TestCase
     Genomics.knowledge_base
   end
 
-  def _test_traverse
+  def test_traverse
     rules = []
     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
+  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
@@ -35,7 +33,13 @@ class TestKnowledgeBaseTraverse < Test::Unit::TestCase
     rules << "?1 pina ?2"
     res =  kb.traverse rules
     assert res.first.include? "?1"
-    iii res.last.first.first.source
+  end
+
+  def test_wildcard_db
+    rules = []
+    rules << "?1 ?db SF3B1 - Method=MI:0006"
+    res =  kb.traverse rules
+    assert res.first.include? "?1"
   end
 end
 

data/test/rbbt/util/test_misc.rb

@@ -512,4 +512,18 @@ eum fugiat quo voluptas nulla pariatur?"
     max = 1000
     assert_equal Misc.sample_large_obj(str, max).length, max+29
   end
+
+  def test_match_value
+    assert Misc.match_value("10", "10")
+    assert Misc.match_value("Hi", /hi/i)
+    assert Misc.match_value("Hi", /Hi/)
+    assert Misc.match_value("Hi", "/Hi/")
+    assert Misc.match_value("Hi", "/hi/i")
+    assert Misc.match_value("15", "<=20")
+    assert Misc.match_value("15", ">14")
+    assert Misc.match_value("15", "! >15")
+    assert Misc.match_value("15", "! >15")
+    assert Misc.match_value("15", [14, 15, 25])
+    assert ! Misc.match_value("15", [14, 25])
+  end
 end

data/test/rbbt/workflow/test_doc.rb

@@ -23,7 +23,8 @@ Task 2
 
   EOF
   def test_parse
-    ddd Workflow.parse_workflow_doc(TEMPLATE)
+    i = Workflow.parse_workflow_doc(TEMPLATE)
+    assert_equal "Title of the template", i[:title]
   end
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.19.10
+  version: 5.19.11
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-01-18 00:00:00.000000000 Z
+date: 2016-01-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -122,6 +122,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: to_regexp
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Utilities for handling tsv files, caches, etc
 email: miguel.vazquez@cnio.es
 executables:
@@ -148,6 +162,7 @@ files:
 - etc/app.d/foundation.rb
 - etc/app.d/grid_system.rb
 - etc/app.d/init.rb
+- etc/app.d/knowledge_bases.rb
 - etc/app.d/resources.rb
 - etc/app.d/workflows.rb
 - lib/rbbt-util.rb