bel 0.5.0 → 0.6.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -3,6 +3,22 @@ All notable changes to bel.rb will be documented in this file. The curated log b
 
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.6.0][0.6.0] - 2016-03-15
+### Fixed
+- Serialization of BEL Script / XBEL can produce incorrect annotation and namespaces references ([Issue #111][111]).
+
+### Changed
+- Separate random sampling from random data in BEL generator ([Issue #105][105]).
+- Improved BEL quoting API. **Deprecated previous API methods.** ([Issue #104][104]).
+- BEL and XBEL translators will now buffer on write to account for all annotation/namespace references. Pass the `-t streaming=true` option to `bel translate` to stream data when the references are consistent.
+
+### Added
+- Added translator read/write option passing from the `bel translate` subcommand.
+
+### Development
+- Added *doctest* Rake task to run YARD `@example` tests in method level documentation.
+- Added gosh commands for running unit, integration and doctests ([Issue #85][85]).
+
 ## [0.5.0][0.5.0] - 2016-02-10
 ### Fixed
 - Fix missing RDF prefixes when converting BEL Script to RDF ([Issue #71][71]).
@@ -75,6 +91,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ### Added
 - Development gem dependencies (i.e. byebug, pry, pry-byebug) for debugging.
 
+[0.6.0]:    https://github.com/OpenBEL/bel.rb/compare/0.5.0...0.6.0
 [0.5.0]:    https://github.com/OpenBEL/bel.rb/compare/0.4.2...0.5.0
 [0.4.2]:    https://github.com/OpenBEL/bel.rb/compare/0.4.1...0.4.2
 [0.4.1]:    https://github.com/OpenBEL/bel.rb/compare/0.4.0...0.4.1
@@ -93,6 +110,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 [68]:       https://github.com/OpenBEL/bel.rb/issues/68
 [71]:       https://github.com/OpenBEL/bel.rb/issues/71
 [82]:       https://github.com/OpenBEL/bel.rb/issues/82
+[85]:       https://github.com/OpenBEL/bel.rb/issues/85
 [86]:       https://github.com/OpenBEL/bel.rb/pull/86
 [90]:       https://github.com/OpenBEL/bel.rb/issues/90
 [91]:       https://github.com/OpenBEL/bel.rb/issues/91
@@ -104,5 +122,8 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 [98]:       https://github.com/OpenBEL/bel.rb/issues/98
 [100]:      https://github.com/OpenBEL/bel.rb/issues/100
 [102]:      https://github.com/OpenBEL/bel.rb/issues/102
+[104]:      https://github.com/OpenBEL/bel.rb/issues/104
+[105]:      https://github.com/OpenBEL/bel.rb/issues/105
+[111]:      https://github.com/OpenBEL/bel.rb/issues/111
 [20150611]: http://resource.belframework.org/belframework/20150611/
 [RDF.rb]:   https://github.com/ruby-rdf/rdf

data/README.md

@@ -75,7 +75,7 @@ the root of the bel.rb tree:
 ## branches
 
 - master branch
-  - Contains stable code. Releases are created from this branch using a tag (e.g. 0.4.0).
+  - Contains stable code. Releases are created from this branch using a tag (e.g. `MAJOR.MINOR.PATCH`).
   - [![Travis CI Build](https://travis-ci.org/OpenBEL/bel.rb.svg?branch=master)](https://travis-ci.org/OpenBEL/bel.rb)
 
 - next branch
@@ -110,7 +110,7 @@ the root of the bel.rb tree:
       plugins
 
 
-    bel 0.4.3
+    bel
     Copyright (C) 2015 OpenBEL
     Apache License, Version 2.0, January 2004
     http://www.apache.org/licenses/
@@ -418,4 +418,6 @@ the root of the bel.rb tree:
     end
 ```
 
+Built with collaboration and a lot of :heart: from the OpenBEL community.
+
 [CHANGELOG]: https://github.com/OpenBEL/bel.rb/blob/master/CHANGELOG.md

data/bin/bel

@@ -2,6 +2,7 @@
 $:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
 require 'erb'
 require 'bel'
+require 'bel/util'
 require 'bel/vendor/trollop'
 
 VERSION_BANNER = <<-VERSION
@@ -232,14 +233,28 @@ Subcommands:
       def run
         parsed_options =
           Trollop::options do
-            synopsis "Translates BEL evidence between file formats."
-            usage    "[OPTIONS]... translate [OPTIONS] FROM_FORMAT TO_FORMAT"
+            synopsis "Translates BEL evidence between formats using translator plugins."
+            usage    "[OPTIONS]... translate [OPTIONS] FROM_TRANSLATOR TO_TRANSLATOR"
 
             opt      :'input-file', 'The file containing evidence data to translate. If not specified the default is to read from STDIN.',
                      :type    => String,
                      :long    => :'input-file',
                      :short   => :i,
                      :default => nil
+
+            opt      :'from-option', 'A "key=value" option to be sent to the FROM_TRANSLATOR.',
+                     :type    => String,
+                     :multi   => true,
+                     :long    => :'from-option',
+                     :short   => :f,
+                     :default => nil
+
+            opt      :'to-option', 'A "key=value" option to be sent to the TO_TRANSLATOR.',
+                     :type    => String,
+                     :multi   => true,
+                     :long    => :'to-option',
+                     :short   => :t,
+                     :default => nil
           end
 
         input_io = which_io(parsed_options[:'input-file'])
@@ -282,12 +297,48 @@ Subcommands:
           Trollop::educate
         end
 
+        from_options = map_kv_options(parsed_options, :'from-option')
+        to_options   = map_kv_options(parsed_options, :'to-option')
+
         begin
-          BEL.translate(input_io, from_format, to_format, $stdout)
+          BEL.translate(
+            input_io,
+            from_format,
+            to_format,
+            $stdout,
+            from_options.merge(to_options) # XXX Merge conflicts.
+          )
         ensure
           $stdout.close
         end
       end
+
+      private
+
+      def map_kv_options(parsed_options, opt)
+        BEL.keys_to_symbols(
+          Hash[
+            parsed_options[opt].map { |opt|
+              key, value = opt.split('=')
+              if !key || !value
+                nil
+              else
+                value =
+                  case value
+                  when "true"
+                    true
+                  when "false"
+                    false
+                  else
+                    value
+                  end
+
+                [key, value]
+              end
+            }.compact
+          ]
+        )
+      end
     end
 
     class UpgradeCommand
@@ -405,11 +456,17 @@ Subcommands:
                    :long        => :translator,
                    :short       => :t,
                    :default     => 'bel'
+
+          opt      :sample,        'Sample namespace values and annotations from BEL resources.',
+                   :long        => :sample,
+                   :short       => :s,
+                   :default     => false
         end
 
         # require BEL generator and include in GenerateCommand
         require 'bel/gen'
         self.class.include(BEL::Gen::Evidence)
+        self.class.include(BEL::Gen::SampleResources) if options[:sample]
 
         # create enumerator of random evidence
         limit       = options[:limit].to_i

data/lib/bel/completion_rule.rb

@@ -234,13 +234,13 @@ module BEL
           :id     => ns_value,
           :type   => :namespace_value,
           :label  => ns_value,
-          :value  => ensure_quotes(ns_value),
+          :value  => quote_if_needed(ns_value),
           :offset => 0
         }
       end
 
       def map_namespace_value_with_prefix(ns, ns_value)
-        quoted_value = ensure_quotes(ns_value)
+        quoted_value = quote_if_needed(ns_value)
 
         if ns
           ns_prefix    = ns.prefix.to_s.upcase

data/lib/bel/evidence_model.rb

@@ -8,3 +8,8 @@ require_relative 'evidence_model/citation'
 require_relative 'evidence_model/summary_text'
 require_relative 'evidence_model/experiment_context'
 require_relative 'evidence_model/metadata'
+
+require_relative 'evidence_model/buffering_evidence_combiner'
+require_relative 'evidence_model/map_references_combiner'
+require_relative 'evidence_model/streaming_evidence_combiner'
+require_relative 'evidence_model/util'

data/lib/bel/evidence_model/bel_parameter.rb

@@ -17,11 +17,6 @@ module BEL
       attr_accessor :ns, :value, :enc
 
       def initialize(ns, value, enc=nil)
-        if !enc && ns.is_a?(BEL::Namespace::NamespaceDefinition)
-          lookup = ns[value]
-          enc    = lookup && lookup.enc
-        end
-
         @enc = enc
         @ns  = ns
         @value = value
@@ -53,7 +48,7 @@ module BEL
         else
           prefix = ''
         end
-        %Q{#{prefix}#{ensure_quotes(@value)}}
+        %Q{#{prefix}#{quote_if_needed(@value)}}
       end
       alias_method :to_s, :to_bel
     end

data/lib/bel/evidence_model/buffering_evidence_combiner.rb

@@ -0,0 +1,182 @@
+require_relative 'hash_map_references'
+
+module BEL
+  module Model
+
+    # EvidenceReferenceCombiner is responsible for disambiguating evidence
+    # with overlapping sets of annotation/namespace references. This can occur
+    # when documents use the same keyword to refer to more than one reference.
+    #
+    # For example, evidence A may be annotated with:
+    #
+    #    {
+    #      :keyword => :Species,
+    #      :type    => :uri,
+    #      :domain  => 'file:///20131211/annotation/species-taxonomy-id.belanno'
+    #    }
+    #
+    # while evidence B may be annotated with:
+    #
+    #    {
+    #      :keyword => :Species,
+    #      :type    => :uri,
+    #      :domain  => 'file:///20150611/annotation/species-taxonomy-id.belanno'
+    #    }
+    #
+    # It is the job of this class to remap references to disambiguate the
+    # keywords.
+    #
+    # @abstract Subclass and override {#map_namespace_reference} to implement
+    # mapping of namespaces.
+    class BufferingEvidenceCombiner
+
+      attr_reader :annotation_references, :namespace_references
+
+      def initialize(evidence_collection)
+        @evidence_collection = evidence_collection
+      end
+
+      def each
+        if block_given?
+          evidence_array, map_references =
+            combine_references(@evidence_collection)
+          @annotation_references = map_references.annotation_references
+          @namespace_references  = map_references.namespace_references
+
+          evidence_array.each do |evidence|
+            if evidence.bel_statement.is_a?(String)
+              evidence.bel_statement = BEL::Model::Evidence.parse_statement(evidence)
+            end
+            yield rewrite_evidence!(evidence, map_references)
+          end
+        else
+          to_enum(:each)
+        end
+      end
+
+      protected
+
+      def combine_references(evidence_collection)
+        annotation_reference_map = {}
+        namespace_reference_map  = {}
+        annotations = []
+        namespaces  = []
+        buffered_evidence = evidence_collection.each.map { |evidence|
+          annotations, remap =
+            BEL::Model.union_annotation_references(
+              annotations,
+              evidence.references.annotations,
+              'incr'
+            )
+          annotation_reference_map.merge!(remap)
+
+          namespaces, remap =
+            BEL::Model.union_namespace_references(
+              namespaces,
+              evidence.references.namespaces,
+              'incr'
+            )
+          namespace_reference_map.merge!(remap)
+
+          evidence
+        }.to_a
+
+        [
+          buffered_evidence,
+          HashMapReferences.new(
+            annotation_reference_map,
+            namespace_reference_map
+          )
+        ]
+      end
+
+      def rewrite_evidence!(evidence, map_references)
+        rewrite_experiment_context!(
+          evidence.experiment_context,
+          evidence.references.annotations,
+          map_references
+        )
+
+        rewrite_statement!(
+          evidence.bel_statement,
+          evidence.references.namespaces,
+          map_references
+        )
+
+        evidence
+      end
+
+      def rewrite_statement!(statement, namespace_references, map_references)
+        keyword_to_reference = Hash[
+          namespace_references.map { |reference|
+            [reference[:keyword], reference]
+          }
+        ]
+
+        sub = statement.subject
+        if sub
+          rewrite_term!(sub, keyword_to_reference, map_references)
+        end
+
+        obj = statement.object
+        if obj
+          case obj
+          when ::BEL::Model::Statement
+            rewrite_statement!(obj, namespace_references, map_references)
+          when ::BEL::Model::Term
+            rewrite_term!(obj, keyword_to_reference, map_references)
+          end
+        end
+      end
+
+      def rewrite_term!(term, keyword_to_reference, map_references)
+        return unless term
+
+        term.arguments.each do |arg|
+          case arg
+          when ::BEL::Model::Parameter
+            if arg.ns
+              prefix =
+                if arg.ns.respond_to?(:prefix)
+                  arg.ns.prefix
+                else
+                  arg.ns[:prefix]
+                end
+              reference     = keyword_to_reference[prefix.to_sym]
+              new_reference = map_references.map_namespace_reference(reference)
+              if new_reference
+                arg.ns = BEL::Namespace::NamespaceDefinition.new(
+                  new_reference[:keyword],
+                  new_reference[:uri]
+                )
+              end
+            end
+          when ::BEL::Model::Term
+            rewrite_term!(arg, keyword_to_reference, map_references)
+          end
+        end
+      end
+
+      def rewrite_experiment_context!(
+        experiment_context,
+        annotation_references,
+        map_references
+      )
+        references = Hash[
+          annotation_references.map { |reference|
+            [reference[:keyword], reference]
+          }
+        ]
+        experiment_context.values.each do |annotation|
+          new_reference = map_references.map_annotation_reference(
+            references[annotation[:name].to_sym]
+          )
+
+          if new_reference
+            annotation[:name] = new_reference[:keyword]
+          end
+        end
+      end
+    end
+  end
+end

data/lib/bel/evidence_model/evidence.rb

@@ -101,6 +101,27 @@ module BEL
         )
         hash
       end
+
+      private
+
+      def parse_statement(bel_statement)
+        namespaces = self.references.namespaces
+        ::BEL::Script.parse(
+          "#{bel_statement}\n",
+          Hash[
+            namespaces.map { |ns|
+              keyword, uri = ns.values_at(:keyword, :uri)
+              sym          = keyword.to_sym
+              [
+                sym,
+                ::BEL::Namespace::NamespaceDefinition.new(sym, uri, uri)
+              ]
+            }
+          ]
+        ).select { |obj|
+          obj.is_a? ::BEL::Model::Statement
+        }.first
+      end
     end
   end
 end