rbbt-util 5.16.3 → 5.17.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 944628eca69d1b9757794dd04d2e1fae618ec30f
-  data.tar.gz: 6c1cb13e51f8efa8e5360b428bf0af8059cd74db
+  metadata.gz: 0077c74cde35411d5404cfef3280cbf2364d916c
+  data.tar.gz: 0c5c8378d8a78fe1341c17cad09d88652714899c
 SHA512:
-  metadata.gz: baf4b9ae49ef200ae206de3aa6b4e2eed9093c653876dafd36f8f4fc06b71ffa89dbb6292a68c1075219193fed77ca539f841b8de3cf6ecd376c3e19c577eaa9
-  data.tar.gz: 8df2ad85ef430be6d054d524cfa5fcab8c3e48be04ad6e47659491c62da16f8a855cf955fb430dfe1e9599b338242a7499c5843b4b4ae5b44e09a7727b4abbea
+  metadata.gz: 42f65b06e9cc69f73efc641c01693ebbeeb2d149888d78a06e3466c5dc09da467c4a36bc4cd6670839de121d1aae51c7d719f6ac6010b93b6ea43c63307d3456
+  data.tar.gz: e4888af1096ab853bf2b30eaa72f98ba3c7c6026914e974f7e4ca49596b389112552ef71f14df6d251ce959faabddcc9b76c613bbe05ff62682923ad68385f92

data/lib/rbbt/association/item.rb

@@ -1,7 +1,7 @@
 require 'rbbt/entity'
 
 module AssociationItem
-  extend Entity
+  extend Object::Entity
 
   annotation :knowledge_base
   annotation :database
@@ -15,11 +15,21 @@ module AssociationItem
     database ? [database, name] * ":" : name
   end 
 
-  property :invert => :single do
-    s,_sep,t= self.partition "~"
-    inverted = self.annotate([t,s] * _sep)
-    inverted.reverse = ! reverse
-    inverted
+  property :invert => :both do
+    if Array === self
+      inverted = self.collect do |item|
+        s,_sep,t= item.partition "~"
+        new = [t,s] * _sep
+      end
+      self.annotate inverted
+      inverted.reverse = ! reverse
+      inverted
+    else
+      s,_sep,t= self.partition "~"
+      inverted = self.annotate([t,s] * _sep)
+      inverted.reverse = ! reverse
+      inverted
+    end
   end
 
   property :namespace => :both do

data/lib/rbbt/knowledge_base/entity.rb

@@ -81,7 +81,7 @@ class KnowledgeBase
   def target_index(name)
     Persist.memory("Target index #{name}: KB directory #{dir}") do
       identifier_files = identifier_files(name)
-      identifier_files.concat Entity.identifier_files(source(name)) if defined? Entity
+      identifier_files.concat Entity.identifier_files(target(name)) if defined? Entity
       identifier_files.uniq!
       identifier_files.collect!{|f| f.annotate(f.gsub(/\bNAMESPACE\b/, namespace))} if namespace
       identifier_files.reject!{|f| f.match(/\bNAMESPACE\b/)}
@@ -100,7 +100,7 @@ class KnowledgeBase
   def identify_target(name, entity)
     return :all if entity == :all
     index = target_index(name)
-    return nil if index.nil?
+    return entity if index.nil?
     Array === entity ? index.values_at(*entity) : index[entity]
   end
 

data/lib/rbbt/knowledge_base/query.rb

@@ -78,5 +78,6 @@ class KnowledgeBase
     setup(name, hash[:parents], true) if hash[:parents]
     hash
   end
+
 end
 

data/lib/rbbt/knowledge_base/traverse.rb

@@ -0,0 +1,105 @@
+require 'rbbt-util'
+require 'rbbt/knowledge_base'
+
+class KnowledgeBase
+
+  class Traverser
+    attr_accessor :rules, :assignments, :matches, :kb
+
+    def initialize(kb, rules = [])
+      @kb = kb
+      @rules = rules
+      @assignments = {}
+      @matches = {}
+    end
+
+    def wildcard(name)
+      return name unless is_wildcard?(name)
+      assignments[name] || name
+    end
+
+    def is_wildcard?(name)
+      name[0] == '?'
+    end
+
+    def identify(db, source, target)
+      source_entities = if is_wildcard? source
+                        assignments[source] || :all
+                      else
+                        kb.identify_source db, source
+                      end
+
+      target_entities = if is_wildcard? target
+                          assignments[target] || :all
+                        else
+                          kb.identify_target db, target
+                        end
+
+      source_entities = [source_entities] unless Array === source_entities or source_entities == :all
+      target_entities = [target_entities] unless Array === target_entities or target_entities == :all
+
+      [source_entities, target_entities]
+    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
+    end
+
+    def find_paths(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 }
+        end
+        
+        if is_wildcard? target
+          assigned = assignments[target]
+          matches = matches.select{|m| assigned.include? m.target }
+        end
+
+        paths[rule] = matches
+      end
+      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)
+    traverser = KnowledgeBase::Traverser.new self, rules
+    traverser.traverse
+  end
+    
+end

data/lib/rbbt/tsv/attach.rb

@@ -195,21 +195,28 @@ module TSV
     other_filename = other.respond_to?(:filename) ? other.filename : other.inspect
     Log.low("Attaching fields:#{Misc.fingerprint fields } from #{other_filename}.")
 
-    case
-    when key_field == other.key_field 
-      Log.debug "Attachment with same key: #{other.key_field}"
-      attach_same_key other, fields
-    when (not in_namespace and self.fields.include?(other.key_field))
-      Log.debug "Found other key field: #{other.key_field}"
-      attach_source_key other, other.key_field, :fields => fields, :one2one => one2one
-    when (in_namespace and self.fields_in_namespace.include?(other.key_field))
-      Log.debug "Found other key field in #{in_namespace}: #{other.key_field}"
-      attach_source_key other, other.key_field, :fields => fields, :one2one => one2one
-    else
-      index = TSV.find_traversal(self, other, options)
-      raise FieldNotFoundError, "Cannot traverse identifiers" if index.nil?
-      Log.debug "Attachment with index: #{other.key_field}"
-      attach_index other, index, fields
+    same_key = true
+    begin
+      case
+      when (key_field == other.key_field and same_key)
+        Log.debug "Attachment with same key: #{other.key_field}"
+        attach_same_key other, fields
+      when (not in_namespace and self.fields.include?(other.key_field))
+        Log.debug "Found other key field: #{other.key_field}"
+        attach_source_key other, other.key_field, :fields => fields, :one2one => one2one
+      when (in_namespace and self.fields_in_namespace.include?(other.key_field))
+        Log.debug "Found other key field in #{in_namespace}: #{other.key_field}"
+        attach_source_key other, other.key_field, :fields => fields, :one2one => one2one
+      else
+        index = TSV.find_traversal(self, other, options)
+        raise FieldNotFoundError, "Cannot traverse identifiers" if index.nil?
+        Log.debug "Attachment with index: #{other.key_field}"
+        attach_index other, index, fields
+      end
+    rescue Exception
+      Log.exception $!
+      same_key = false
+      retry
     end
     Log.debug("Attachment of fields:#{Misc.fingerprint fields } from #{other.filename.inspect} finished.")
 

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

@@ -535,6 +535,9 @@ 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}) 
@@ -547,6 +550,9 @@ module TSV
                     when Hash
                       max = Misc.process_options(bar, :max) || max
                       Log::ProgressBar.new_bar(max, bar) 
+                    when Log::ProgressBar
+                      bar.max ||= guess_max(obj)
+                      bar
                     else
                       bar
                     end

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

@@ -4,10 +4,10 @@ require 'rbbt/util/log/progress/report'
 module Log
   class ProgressBar
 
-    attr_accessor :max, :ticks, :frequency, :depth, :desc
+    attr_accessor :max, :ticks, :frequency, :depth, :desc, :file
     def initialize(max = nil, options = {})
       options = Misc.add_defaults options, :depth => 0, :num_reports => 100, :desc => "Progress", :io => STDERR, :severity => Log.severity
-      depth, num_reports, desc, io, severity = Misc.process_options options, :depth, :num_reports, :desc, :io, :severity
+      depth, num_reports, desc, io, severity, file = Misc.process_options options, :depth, :num_reports, :desc, :io, :severity, :file
 
       @max = max
       @ticks = 0
@@ -17,6 +17,7 @@ module Log
       @last_percent = nil
       @depth = depth
       @desc = desc
+      @file = file
     end
 
     def percent

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

@@ -90,6 +90,11 @@ module Log
       str
     end
 
+    def save
+      info = {:start => @start, :last_time => @last_time, :last_count => @last_count, :last_percent => @last_percent, :desc => @desc, :ticks => @ticks, :max => @max}
+      Open.write(@file, info.to_yaml)
+    end
+
     def report(io = STDERR)
       if Log::LAST != "progress"
         length = Log::ProgressBar.cleanup_bars
@@ -106,6 +111,7 @@ module Log
       @last_time = Time.now
       @last_count = ticks
       @last_percent = percent if max
+      save if @file
     end
 
     def done(io = STDERR)
@@ -121,6 +127,7 @@ module Log
       @last_time = @start
       done_msg << " (" << thr_msg << ")"
       print(io, up_lines(@depth) << done_msg << down_lines(@depth)) 
+      Open.rm @file if @file and Open.exists? @file
     end
   end
 end

data/lib/rbbt/workflow/accessor.rb

@@ -211,8 +211,8 @@ class Step
     end
   end
 
-  def self.log_progress(status, options, path, &block)
-    options = Misc.add_defaults options, :severity => Log::INFO
+  def self.log_progress(status, options = {}, path = nil, &block)
+    options = Misc.add_defaults options, :severity => Log::INFO, :file => path
     max = Misc.process_options options, :max
     Log::ProgressBar.with_bar(max, options) do |bar|
       begin
@@ -225,6 +225,14 @@ class Step
     end
   end
 
+  def log_progress(status, options = {}, &block)
+    Step.log_progress(status, options, file(:progress), &block)
+  end
+
+  def progress_bar(msg, options = {})
+    Log::ProgressBar.new nil, {:desc => msg, :file => file(:progress)}.merge(options)
+  end
+
   def self.log(status, message, path, &block)
     if block
       if Hash === message

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

@@ -134,6 +134,9 @@ class Step
       dependency.dup_inputs
     end
 
+    return if @seen.empty?
+
+    log :dependencies, "#{Log.color :magenta, "Dependencies"} #{Log.color :yellow, task.name.to_s || ""}"
     @seen.each do |dependency| 
       next if dependency == self
       next unless dependencies.include? dependency

data/share/rbbt_commands/app/template

@@ -1,66 +1,66 @@
 #!/usr/bin/env ruby
 
-require 'rbbt'
-require 'rbbt/resource'
-require 'rbbt-util'
 require 'rbbt/util/simpleopt'
+require 'rbbt/workflow'
 
-options = SOPT.get "-e--environment*:-p--port*:-s--server*:-h--host*:-f--finder"
-options[:Port] ||= options[:port]
+require 'zurb-foundation'
+require 'modular-scale'
 
-file = ARGV.shift
+require 'rbbt/rest/main'
+require 'rbbt/rest/entity'
+require 'rbbt/rest/workflow'
+require 'rbbt/rest/file_server'
+require 'rbbt/rest/knowledge_base'
+require 'rbbt/rest/helpers'
+require 'rbbt/rest/web_tool'
 
-load Rbbt.etc['app.d/init.rb'].find
+options = SOPT.get "-e--environment*:-p--port*:-s--server*:-b--bind*:-e--environment*:-R--RServe_session*:--finder:--views*:-w--workflows*"
+
+template = ARGV.first
 
-$class_name = class_name = "SingleTemplate"
+template = template.sub('.haml','')
 
-$app = app = eval "class #{class_name} < Sinatra::Base; self end"
+ENV["RBBT_FINDER"] = "true" if options.include?(:finder)
+ENV["RServe-session"] = options[:RServe_session] 
 
-#$LOAD_PATH.unshift('lib')
+raise rbbt_usage unless template
 
-#{{{ PRE
-Log.info{"Loading: " << Rbbt.etc['app.d/pre.rb'].find if Rbbt.etc['app.d/pre.rb'].exists?}
-load Rbbt.etc['app.d/pre.rb'].find if Rbbt.etc['app.d/pre.rb'].exists?
+$title = File.basename(template)
 
-app.get '/' do
-  file = file.sub(/\.haml/,'')
-  template_render(file)
+load Rbbt.etc['app.d/init.rb'].find
+
+app = class SingleTemplate < Sinatra::Base; self end
+
+if options[:workflows]
+  app.register Sinatra::RbbtRESTWorkflow
+  options[:workflows].split(/[\s,]+/).each do |name|
+    wf = Workflow.require_workflow name
+    app.add_workflow wf, :all
+  end
 end
 
-#{{{ BASE
-app.class_eval do
-  Log.info{"Loading: " << Rbbt.etc['app.d/base.rb'].find}
-  eval Rbbt.etc['app.d/base.rb'].read, nil, Rbbt.etc['app.d/base.rb'].find
+app.register Sinatra::RbbtRESTKnowledgeBase
+
+app.helpers Sinatra::RbbtMiscHelpers
+app.helpers Sinatra::RbbtToolHelper
+
+app.get '/' do
+  template_render(template, @clean_params)
 end
+app.instance_eval Rbbt.etc['app.d/base.rb'].read
+app.use Rack::Deflater
 
-#{{{ RESOURCES
-Log.info{"Loading: " << Rbbt.etc['app.d/resources.rb'].find}
 load Rbbt.etc['app.d/resources.rb'].find
 
-#{{{ ENTITIES
-Log.info{"Loading: " << Rbbt.etc['app.d/entities.rb'].find}
-load Rbbt.etc['app.d/entities.rb'].find
-
-#{{{ FINDER
 app.class_eval do
-  Log.info{"Loading: " << Rbbt.etc['app.d/finder.rb'].find}
   eval Rbbt.etc['app.d/finder.rb'].read
 end
 
-#{{{ POST
-Log.info{"Loading: " << Rbbt.etc['app.d/post.rb'].find if Rbbt.etc['app.d/post.rb'].exists?}
-load Rbbt.etc['app.d/post.rb'].find if Rbbt.etc['app.d/post.rb'].exists?
-
-#{{{ RUN
-$title = class_name
-require 'rack'
-
-ENV["RBBT_FINDER"] = "true" if options.include?(:finder)
-ENV["RACK_ENV"] = options[:environment] if options.include?(:environment)
+Sinatra::RbbtRESTMain.add_resource_path(Path.setup('/home/mvazquezg/'), true)
 
-RbbtRESTHelpers.template_resources.unshift Path.setup(File.expand_path(File.dirname(file)))
 
-app.port = options[:port] if options[:port]
-app.server = options[:server] if options[:server]
-app.environment = options[:environment] if options[:environment]
-app.run!
+SingleTemplate.port = options[:port] || 4567
+SingleTemplate.bind = options[:bind] || "0.0.0.0"
+SingleTemplate.environment = options[:environment] || "development"
+SingleTemplate.server = options[:server] if options[:server]
+SingleTemplate.run!

data/share/rbbt_commands/workflow/server

@@ -12,8 +12,9 @@ require 'rbbt/rest/workflow'
 require 'rbbt/rest/file_server'
 require 'rbbt/rest/knowledge_base'
 require 'rbbt/rest/helpers'
+require 'rbbt/rest/web_tool'
 
-options = SOPT.get "-e--environment*:-p--port*:-s--server*:-b--bind*:-e--environment*:-R--RServe_session*:--finder:--views*"
+options = SOPT.get "-e--environment*:-p--port*:-s--server*:-b--bind*:-e--environment*:-R--RServe_session*:--finder:--views*:-w--workflows*"
 
 workflow = ARGV.first
 
@@ -32,6 +33,7 @@ app = class WorkflowRest < Sinatra::Base; self end
 
 app.register Sinatra::RbbtRESTWorkflow
 app.register Sinatra::RbbtRESTKnowledgeBase
+app.helpers Sinatra::RbbtToolHelper
 
 app.get '/' do
   redirect to(File.join('/', wf.to_s))
@@ -46,6 +48,13 @@ app.class_eval do
 end
 
 WorkflowRest.add_workflow wf, :all
+if options[:workflows]
+  options[:workflows].split(/[\s,]+/).each do |name|
+    _wf = Workflow.require_workflow name
+    WorkflowRest.add_workflow _wf, :all
+  end
+end
+
 
 if options[:views] and not options[:views].empty?
   Sinatra::RbbtRESTMain.add_resource_path(Path.setup(options[:views]), true)

data/test/rbbt/knowledge_base/test_traverse.rb

@@ -0,0 +1,19 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/knowledge_base/traverse'
+require 'rbbt/workflow'
+
+Workflow.require_workflow "Genomics"
+class TestKnowledgeBaseTraverse < Test::Unit::TestCase
+  def kb
+    Genomics.knowledge_base
+  end
+
+  def test_traverse
+    rules = []
+    rules << "SF3B1 pina ?1 - Method=MI:0006"
+    rules << "TP53 pina ?1"
+    res =  kb.traverse rules
+    assert res.first.include? "?1"
+  end
+end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.16.3
+  version: 5.17.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-02-12 00:00:00.000000000 Z
+date: 2015-02-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -170,6 +170,7 @@ files:
 - lib/rbbt/knowledge_base/query.rb
 - lib/rbbt/knowledge_base/registry.rb
 - lib/rbbt/knowledge_base/syndicate.rb
+- lib/rbbt/knowledge_base/traverse.rb
 - lib/rbbt/monitor.rb
 - lib/rbbt/packed_index.rb
 - lib/rbbt/persist.rb
@@ -346,6 +347,7 @@ files:
 - test/rbbt/knowledge_base/test_query.rb
 - test/rbbt/knowledge_base/test_registry.rb
 - test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_traverse.rb
 - test/rbbt/persist/test_tsv.rb
 - test/rbbt/persist/tsv/test_cdb.rb
 - test/rbbt/persist/tsv/test_kyotocabinet.rb
@@ -465,6 +467,7 @@ test_files:
 - test/rbbt/test_packed_index.rb
 - test/rbbt/entity/test_identifiers.rb
 - test/rbbt/test_association.rb
+- test/rbbt/knowledge_base/test_traverse.rb
 - test/rbbt/knowledge_base/test_registry.rb
 - test/rbbt/knowledge_base/test_entity.rb
 - test/rbbt/knowledge_base/test_enrichment.rb