bel 0.4.0 → 0.4.1

checksums.yaml

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

@@ -3,6 +3,18 @@ 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/).
 
+## [0.4.1][0.4.1] - 2015-12-17
+### Added
+- Updated `find` API of `BEL::Resource::Namespaces` and `BEL::Resource::Namespace` to find by string representing a URI.
+
+### Fixed
+- [Development] Install `pry-byebug` only for `ruby` platforms. This allows development on JRuby.
+- [Development] No-op `rake compile` when running on JRuby. Report informative message when compiling on JRuby.
+
+### Changed
+- Complete BEL namespaces and namespace values using the Namespaces API backed by RDF data.
+- Enable :exclude_identifier_schemes option for BEL completion to disallow namespace value results that report an identifier as their preferred name. This is allowed if the namespace prefix is first provided (e.g. "EG:AKT" will find "EG:207").
+
 ## [0.4.0][0.4.0] - 2015-12-14
 ### Fixed
 - Improved conversion of evidence to JSON Evidence format.
@@ -45,6 +57,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ### Added
 - Development gem dependencies (i.e. byebug, pry, pry-byebug) for debugging.
 
+[0.4.1]:    https://github.com/OpenBEL/bel.rb/compare/0.4.0...0.4.1
 [0.4.0]:    https://github.com/OpenBEL/bel.rb/compare/0.3.3...0.4.0
 [0.3.2]:    https://github.com/OpenBEL/bel.rb/compare/0.3.1...0.3.2
 [0.3.3]:    https://github.com/OpenBEL/bel.rb/compare/0.3.2...0.3.3

data/lib/bel/completion.rb

@@ -12,9 +12,11 @@ module BEL
     # otherwise the +to_s+ method is called. An empty +bel_expression+ will
     # return all BEL functions as possible completions.
     #
-    # If +search+ is +nil+ then namespace values will not be provided as
-    # completion. +search+ is expected to provide +#search+ and
-    # +#search_namespace+ methods.
+    # A {BEL::Resource::Search} plugin must be provided that provides
+    # completions for namespaces and namespace values.
+    #
+    # A {BEL::Resource::Namespaces} API must be provided to resolve namespace
+    # properties given a URI.
     #
     # If +position+ is +nil+ then its assumed to be the last index of
     # +bel_expression+ otherwise the +to_i+ method is called.
@@ -28,7 +30,14 @@ module BEL
     # provide namespace value completions
     # @param position         [responds to #to_i] the position to complete from
     # @return [Array<Completion>]
-    def self.complete(bel_expression, search = nil, position = nil)
+    def self.complete(bel_expression, search, namespaces, position = nil)
+      raise ArgumentError.new(
+        "search should be a BEL::Resource::Search plugin implementation"
+      ) unless search
+      raise ArgumentError.new(
+        "namespaces should be a BEL::Resource::Namespaces object"
+      ) unless namespaces
+
       bel_expression = (bel_expression || '').to_s
       position = (position || bel_expression.length).to_i
       if position < 0 or position > bel_expression.length
@@ -47,7 +56,11 @@ module BEL
       options = {
         :search => search
       }
-      BEL::Completion::run_rules(tokens, active_index, active_token, options)
+      BEL::Completion::run_rules(
+        tokens, active_index, active_token,
+        :search     => search,
+        :namespaces => namespaces
+      )
     end
   end
 end

data/lib/bel/completion_rule.rb

@@ -1,7 +1,6 @@
 require_relative 'language'
 require_relative 'namespace'
 require_relative 'quoting'
-require 'uri'
 
 module BEL
   module Completion
@@ -182,8 +181,9 @@ module BEL
       include BEL::Quoting
 
       def _apply(token_list, active_token, active_token_index, options = {})
-        search = options.delete(:search)
-        return EMPTY_MATCH if not search or token_list.empty?
+        search     = options.delete(:search)
+        namespaces = options.delete(:namespaces)
+        return EMPTY_MATCH if !search || !namespaces || token_list.empty?
 
         if active_token.type == :IDENT && active_token.value.length > 1
           previous_token = token_list[active_token_index - 1]
@@ -191,16 +191,16 @@ module BEL
             # search within a namespace
             prefix_token = token_list[active_token_index - 2]
             if prefix_token and prefix_token.type == :IDENT
-              namespace = BEL::Namespace::NAMESPACE_LATEST[prefix_token.value.to_sym]
+              namespace = namespaces.find(prefix_token.value.downcase).first
               if namespace
-                scheme_uri = namespace[1]
                 return search.search(
                   "#{active_token.value}*",
                   :namespace_concept,
-                  URI(scheme_uri),
+                  namespace.uri.to_s,
                   nil,
                   :start => 0,
-                  :size  => 10
+                  :size  => 10,
+                  :exclude_identifier_schemes => false
                 ).
                   map { |search_result|
                     map_namespace_value(search_result.pref_label)
@@ -214,10 +214,12 @@ module BEL
               nil,
               nil,
               :start => 0,
-              :size  => 10
+              :size  => 10,
+              :exclude_identifier_schemes => true
             ).
               map { |search_result|
-                map_namespace_value(search_result.pref_label)
+                ns = namespaces.find(search_result.scheme_uri).first
+                map_namespace_value_with_prefix(ns, search_result.pref_label)
               }.to_a
           end
         end
@@ -236,6 +238,24 @@ module BEL
           :offset => 0
         }
       end
+
+      def map_namespace_value_with_prefix(ns, ns_value)
+        quoted_value = ensure_quotes(ns_value)
+
+        if ns
+          ns_prefix    = ns.prefix.to_s.upcase
+          ns_value     = "#{ns_prefix}:#{ns_value}"
+          quoted_value = "#{ns_prefix}:#{quoted_value}"
+        end
+
+        {
+          :id     => ns_value,
+          :type   => :namespace_value,
+          :label  => ns_value,
+          :value  => quoted_value,
+          :offset => 0
+        }
+      end
     end
   end
 end

data/lib/bel/resource.rb

@@ -15,6 +15,8 @@ module BEL
       property :inScheme
       property :orthologousMatch
     end
+
+    FULL_URI_REGEX = /\A#{URI::regexp}\z/
   end
 end
 

data/lib/bel/resource/namespace.rb

@@ -55,14 +55,14 @@ module BEL
         # nil input always yield nil
         return nil if value == nil
 
-        # RDF::URI input handled as a special case
-        return find_namespace_value_uri(value) if value.is_a?(RDF::URI)
-
         # input handled as literal identifier; empty literals match in a
         # pattern as if it was nil so return nil if empty string
         vstr  = value.to_s
         return nil if vstr.empty?
 
+        # URI handled by regex match on string
+        return find_namespace_value_uri(vstr) if vstr =~ FULL_URI_REGEX
+
         # match input as namespace value prefLabel
 				vlit  = RDF::Literal(vstr)
 				label = value_query(
@@ -86,15 +86,16 @@ module BEL
 				return NamespaceValue.new(@rdf_repository, title.subject) if title
       end
 
-      def find_namespace_value_uri(uri)
+      def find_namespace_value_uri(uri_s)
+        subject            = RDF::URI(uri_s)
         in_namespace_check = @rdf_repository.has_statement?(
-          RDF::Statement(uri, RDF::SKOS.inScheme, @uri)
+          RDF::Statement(subject, RDF::SKOS.inScheme, @uri)
         )
         return nil if !in_namespace_check
 
-        type_check = RDF::Statement(uri, RDF.type, BELV.NamespaceConcept)
+        type_check = RDF::Statement(subject, RDF.type, BELV.NamespaceConcept)
 				if @rdf_repository.has_statement?(type_check)
-          return NamespaceValue.new(@rdf_repository, uri)
+          return NamespaceValue.new(@rdf_repository, subject)
         end
 			end
 

data/lib/bel/resource/namespaces.rb

@@ -40,14 +40,14 @@ module BEL
         # nil input always yield nil
         return nil if namespace == nil
 
-        # RDF::URI input handled as a special case
-        return find_namespace_uri(namespace) if namespace.is_a?(RDF::URI)
-
-        # input handled as literal identifier; empty literals will match
-        # in a pattern as if it was nil so return nil if empty string
-        nstr  = namespace.to_s
+        # empty literals will match in a pattern as if it was nil
+        # so return nil if empty string
+        nstr = namespace.to_s
         return nil if nstr.empty?
 
+        # URI handled by regex match on string
+        return find_namespace_uri(nstr) if nstr =~ FULL_URI_REGEX
+
         # match input as namespace prefix
 				nlit   = RDF::Literal(nstr)
 				prefix = namespace_query(
@@ -64,10 +64,11 @@ module BEL
 				return Namespace.new(@rdf_repository, label.subject) if label
       end
 
-      def find_namespace_uri(uri)
-        type_check = RDF::Statement(uri, RDF.type, BELV.NamespaceConceptScheme)
+      def find_namespace_uri(uri_s)
+        subject    = RDF::URI(uri_s)
+        type_check = RDF::Statement(subject, RDF.type, BELV.NamespaceConceptScheme)
 				if @rdf_repository.has_statement?(type_check)
-          return Namespace.new(@rdf_repository, uri)
+          return Namespace.new(@rdf_repository, subject)
         end
 			end
 

data/lib/bel/version.rb

@@ -1,3 +1,3 @@
 module BEL
-  VERSION = '0.4.0'
+  VERSION = '0.4.1'
 end

metadata

@@ -1,34 +1,34 @@
 --- !ruby/object:Gem::Specification
 name: bel
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.4.1
 platform: ruby
 authors:
 - Anthony Bargnesi
 - Natalie Catlett
 - Nick Bargnesi
 - William Hayes
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2015-12-14 00:00:00.000000000 Z
+date: 2015-12-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: ffi
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.9.8
-  type: :runtime
+  name: ffi
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.9.8
-description: " The BEL gem allows the reading, writing, and processing of BEL (Biological
-  Expression Language) with a natural DSL. "
+description: " The BEL gem allows the reading, writing, and processing of BEL (Biological\
+  \ Expression Language) with a natural DSL. "
 email:
 - abargnesi@selventa.com
 - ncatlett@selventa.com
@@ -167,7 +167,7 @@ homepage: https://github.com/OpenBEL/bel.rb
 licenses:
 - Apache-2.0
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options:
 - "--title"
 - BEL Ruby Documentation
@@ -201,10 +201,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.4.5.1
-signing_key: 
+rubyforge_project:
+rubygems_version: 2.4.8
+signing_key:
 specification_version: 4
 summary: Process BEL with ruby.
 test_files: []
-has_rdoc: 
+has_rdoc: