bel 0.3.3 → 0.4.0.beta1

checksums.yaml

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

@@ -1,5 +1,4 @@
-bel ruby
-========
+# bel ruby
 
 [![Gem Version](https://badge.fury.io/rb/bel.svg)](http://badge.fury.io/rb/bel)
 
@@ -32,18 +31,65 @@ Install / Build: See [INSTALL](INSTALL.md).
 
 A changelog is maintained at [CHANGELOG][CHANGELOG].
 
-branches
---------
+## development
+
+Developing on bel.rb requires a few steps.
+
+1. [Install Ruby](INSTALL_RUBY.md).
+2. Clone this repository:
+
+    ```
+    git@github.com:OpenBEL/bel.rb.git
+    ```
+
+3. Change to repository directory. Install bel.rb's dependencies (including development dependencies):
+
+    ```
+    cd bel.rb; ./scripts/gem-install-devdeps.sh
+    ```
+
+4. Build C extension (i.e. [libbel parser](https://github.com/OpenBEL/libbel)) using Rake:
+
+    ```
+    rake compile
+    ```
+
+  This will build the C shared library you will need to use the C-based parser.
+
+  Note: Windows users will need to install the [RubyInstaller DevKit](https://github.com/oneclick/rubyinstaller/wiki/Development-Kit) to build the C extension.
+
+### isolated development
+
+During development, it is recommended to isolate bel.rb from any existing user
+or system gems. This will help keep gems used during development entirely
+separate from all others.
+
+To accomplish this, set ``BR_ISOLATE`` to ``"yes"`` in ``env.sh.custom``, at
+the root of the bel.rb tree:
+
+```bash
+    export BR_ISOLATE="yes"
+```
+
+
+## branches
 
 - master branch
+  - Contains stable code. Releases are created from this branch using a tag (e.g. 0.3.3).
   - [![Travis CI Build](https://travis-ci.org/OpenBEL/bel.rb.svg?branch=master)](https://travis-ci.org/OpenBEL/bel.rb)
 
 - next branch
+  - Contains unstable code. Commits should be merged into master after it stabilizes.
   - [![Build Status for next branch](https://travis-ci.org/OpenBEL/bel.rb.svg?branch=next)](https://travis-ci.org/OpenBEL/bel.rb)
 
+## contributors
+
+- [@abargnesi](https://github.com/abargnesi) (Maintainer)
+- [@nbargnesi](https://github.com/nbargnesi) (Maintainer)
+- [@ncatlett](https://github.com/ncatlett)   (Contributor)
+- [@wshayes](https://github.com/wshayes)     (Contributor)
 
-executable commands
--------------------
+## executable commands
 
 **bel**: A single executable command with subcommands.
 
@@ -154,8 +200,7 @@ executable commands
 ```
 
 
-api examples
-------------
+## api examples
 
 **Use OpenBEL namespaces from the latest release.**
 

data/bel.gemspec

@@ -55,22 +55,17 @@ Gem::Specification.new do |spec|
   spec.extensions              << 'ext/mri/extconf.rb'
   spec.required_ruby_version    = '>= 2.0.0'
 
-  # runtime
-  spec.add_dependency             'ffi',           '1.9.8'
+  spec.add_runtime_dependency 'ffi', '1.9.8'
 
-  # test rdf functionality
-  spec.add_development_dependency 'addressable',   '~> 2.3'
-  spec.add_development_dependency 'rdf',           '~> 1.1'
-  spec.add_development_dependency 'rdf-turtle',    '~> 1.1'
-  spec.add_development_dependency 'uuid',          '~> 2.3'
-
-  # development gems
-  spec.add_development_dependency 'minitest',      '~> 5.7'
-  spec.add_development_dependency 'rake',          '~> 10.4'
-  spec.add_development_dependency 'rake-compiler', '~> 0.9'
-  spec.add_development_dependency 'rdoc',          '~> 4.2'
-  spec.add_development_dependency 'rspec',         '~> 3.2'
-  spec.add_development_dependency 'yard',          '~> 0.8'
+  # Example post-install message.
+  #
+  # These aren't real BEL-related gems, but if we can sneak the names passed
+  # abargnesi, maybe one day... ;)
+  # spec.post_install_message = %q(
+  # -- bel.rb notice --
+  # Install any of these additional gems for more functionality:
+  # bel-rdf, clapper, carillon, peal, ...
+  # )
 end
 # vim: ts=2 sw=2:
 # encoding: utf-8

data/bin/bel

@@ -1,5 +1,5 @@
 #!/usr/bin/env ruby
-$: << File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib')
+$:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
 require 'erb'
 require 'bel'
 require 'bel/vendor/trollop'
@@ -260,7 +260,7 @@ Subcommands:
 
         from_format, to_format = ARGV
 
-        from = BEL::Extension::Format.formatters(from_format)
+        from = BEL.translator(from_format)
         unless from
           $stderr.puts(
             from_format ?
@@ -271,7 +271,7 @@ Subcommands:
           Trollop::educate
         end
 
-        to   = BEL::Extension::Format.formatters(to_format)
+        to   = BEL.translator(to_format)
         unless to
           $stderr.puts(
             to_format ?
@@ -283,7 +283,7 @@ Subcommands:
         end
 
         begin
-          BEL::Format.translate(input_io, from_format, to_format, $stdout)
+          BEL.translate(input_io, from_format, to_format, $stdout)
         ensure
           $stdout.close
         end
@@ -326,6 +326,65 @@ Subcommands:
         require_relative 'bel_upgrade'
       end
     end
+
+    class PluginsCommand
+
+      def initialize(global_options)
+        @global_options = global_options
+      end
+
+      def run
+        options = Trollop::options do
+          synopsis "Interact with available plugins."
+          usage    "[OPTIONS]... plugins [OPTIONS]"
+          opt      :list,  'Lists available plugins',
+                   :long    => :list,
+                   :short   => :l,
+                   :default => true
+        end
+
+        if options[:list]
+          $stdout.puts "RDF Repository plugins"
+          $stdout.puts "----------------------"
+          $stdout.puts
+          BEL::RdfRepository.plugins.
+            values.
+            sort_by { |plugin| plugin.name}.
+            each do |plugin|
+              $stdout.puts %Q{
+                Name:        #{plugin.name}
+                Description: #{plugin.description}
+              }.gsub(%r{^\s+}, ' ')
+            end
+
+          $stdout.puts "Resource Search plugins"
+          $stdout.puts "-----------------------"
+          $stdout.puts
+          BEL::Resource::Search.plugins.
+            values.
+            sort_by { |plugin| plugin.name}.
+            each do |plugin|
+              $stdout.puts %Q{
+                Name:        #{plugin.name}
+                Description: #{plugin.description}
+              }.gsub(%r{^\s+}, ' ')
+            end
+
+          $stdout.puts "Translator plugins"
+          $stdout.puts "------------------"
+          $stdout.puts
+          BEL::Translator.plugins.
+            values.
+            sort_by { |plugin| plugin.name}.
+            each do |plugin|
+              $stdout.puts %Q{
+                Name:        #{plugin.name}
+                Description: #{plugin.description}
+              }.gsub(%r{^\s+}, ' ')
+            end
+        end
+      end
+    end
   end
 end
 

data/bin/bel2rdf.rb

@@ -13,7 +13,7 @@
 # Format option
 # usage: bel2rdf --bel [FILE] --format [ntriples | nquads | turtle]
 
-$: << File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib')
+$:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
 require 'bel'
 require 'optparse'
 require 'set'

data/bin/bel_compare.rb

@@ -1,7 +1,7 @@
 #!/usr/bin/env ruby
 # vim: ts=2 sw=2
 
-$: << File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib')
+$:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
 require 'optparse'
 require 'bel'
 include BEL::Language

data/bin/bel_parse.rb

@@ -7,7 +7,7 @@
 # From standard in
 # usage: echo "<BEL DOCUMENT STRING>" | bel_parse
 
-$: << File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib')
+$:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
 require 'bel'
 require 'optparse'
 

data/bin/bel_rdfschema.rb

@@ -2,7 +2,7 @@
 # bel_rdfschema: Dump RDF schema for BEL.
 # usage: bel_rdfschema --format [ntriples | nquads | turtle]
 
-$: << File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib')
+$:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
 require 'bel'
 require 'optparse'
 require 'set'

data/bin/bel_summarize.rb

@@ -1,7 +1,7 @@
 #!/usr/bin/env ruby
 # vim: ts=2 sw=2
 
-$: << File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib')
+$:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
 require 'bel'
 require 'csv'
 require 'optparse'

data/bin/bel_upgrade.rb

@@ -7,7 +7,7 @@
 # From standard in
 # usage: echo "<BEL DOCUMENT STRING>" | bel_upgrade -c file.json
 
-$: << File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib')
+$:.unshift(File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
 require 'bel'
 require 'json'
 require 'optparse'

data/lib/bel.rb

@@ -1,12 +1,15 @@
 require_relative 'bel/version'
+require_relative 'bel/vendor/little-plugger'
 require_relative 'bel/language'
 require_relative 'bel/namespace'
 require_relative 'bel/util'
 
-require_relative 'bel/extension'
-require_relative 'bel/extension_format'
 require_relative 'bel/evidence_model'
-require_relative 'bel/format'
+require_relative 'bel/translator'
+require_relative 'bel/translate'
+
+require_relative 'bel/rdf_repository'
+require_relative 'bel/resource'
 
 require_relative 'bel/script'
 
@@ -17,13 +20,8 @@ require_relative 'bel/completion'
 include BEL::Language
 include BEL::Namespace
 
-BEL::Extension.load_extension('jgf', 'json/json', 'bel', 'xbel')
-
-begin
-  BEL::Extension.load_extension('rdf/rdf')
-rescue LoadError => e
-  # No RDF support.
-  # TODO Report extension load failure.
+module BEL
+  extend BEL::Translate::ClassMethods
 end
 # vim: ts=2 sw=2:
 # encoding: utf-8

data/lib/bel/completion.rb

@@ -13,7 +13,8 @@ module BEL
     # return all BEL functions as possible completions.
     #
     # If +search+ is +nil+ then namespace values will not be provided as
-    # completion. +search+ is expected to implement {IdentifierSearch}.
+    # completion. +search+ is expected to provide +#search+ and
+    # +#search_namespace+ methods.
     #
     # If +position+ is +nil+ then its assumed to be the last index of
     # +bel_expression+ otherwise the +to_i+ method is called.
@@ -23,7 +24,7 @@ module BEL
     #
     # @param bel_expression   [responds to #to_s] the bel expression to
     # complete on
-    # @param search           [IdentifierSearch] the search object used to
+    # @param search           [#search_namespace, #search] the search object used to
     # provide namespace value completions
     # @param position         [responds to #to_i] the position to complete from
     # @return [Array<Completion>]

data/lib/bel/completion/value_match_rule.rb

@@ -0,0 +1,10 @@
+module BEL
+  module Completion
+
+    class ValueMatch
+
+      def call(ast)
+      end
+    end
+  end
+end

data/lib/bel/evidence_model/citation.rb

@@ -1,46 +1,40 @@
 module BEL
   module Model
 
-    # A Citation provides a reference to the resource containing the
-    # {Evidence} information. The fields are defined as:
+    # A Citation describes a cited reference which {Evidence} is derived from.
     #
-    # - +date+
-    #   - The date represents when the article was published.
-    # - +authors+
-    #   - The authors refer to the authors of the article.
-    #
-    # @attr [String] type the type of the article commonly defined by
-    #       +"PubMed"+, +"Journal"+, +"Book"+, or +"Online Resource"+
-    # @attr [String] name the name of the article
-    # @attr [String] id the identifier of the article. For example, for a
-    #       +"PubMed"+ type the identifier is the PMID (i.e. 12102192)
-    # @attr [String] date the date when the article was published
-    # @attr [String] authors the authors of the article
-    # @attr [String] comment a comment on the citation
-    class Citation < Struct.new(
-      :type,
-      :name,
-      :id,
-      :date,
-      :authors,
-      :comment
-    )
+    # @attr [String] type the type of resource the cited material appears in
+    #       (e.g. PubMed, Journal, Book, Online Resource, etc...)
+    # @attr [String] name the name of the cited resource
+    # @attr [String] id the unique identifier for the cited resource. For
+    #       example, a +"PubMed"+ type should have a PMID (i.e. 12102192).
+    # @attr [String] date the date the resource was published
+    # @attr [String] authors the authors of the resource
+    # @attr [String] comment an additional comment related to this resource
+    class Citation
 
-      # Creates a {Citation} struct from a +Hash+.
-      # @param [Hash] fields the citation fields to populate based on hash
-      #        keys
-      # @example Create a minimal {Citation}.
-      #   Citation.create(
-      #     {
-      #       :type => 'PubMed',
-      #       :name => 'Biocompatibility study of biological tissues fixed
-      #                 by a natural compound (reuterin) produced by
-      #                 Lactobacillus reuteri.',
-      #       :id   => '12102192'
-      #     }
+      MEMBER_ORDER = %i(type name id date authors comment)
+
+      attr_accessor(*MEMBER_ORDER)
+
+      # Creates a {Citation} object from variable arguments.
+      #
+      # @param [Array<Object>] args Argument array of Object; If the array
+      #        contains a single value then it is expected to either respond
+      #        to +:each+ (according to #MEMBER_ORDER) or +:each_pair+
+      #        (keys matching that of #MEMBER_ORDER). If the array has
+      #        multiple values then they are set sequentially according to
+      #        #MEMBER_ORDER.
+      # @example Create an empty {Citation}.
+      #   Citation.new
+      # @example Create a minimal {Citation} by positional members.
+      #   Citation.new('PubMed', 'Biocompatibility study of...', '12102192')
+      # @example Create a minimal {Citation} by positional members in array.
+      #   Citation.new(
+      #     ['PubMed', 'Biocompatibility study of...', '12102192']
       #   )
-      # @example Create a full {Citation}.
-      #   Citation.create(
+      # @example Create a full {Citation} by hash using keys for members.
+      #   Citation.new(
       #     {
       #       :type    => 'PubMed',
       #       :name    => 'Biocompatibility study of biological tissues fixed
@@ -52,17 +46,81 @@ module BEL
       #       :comment => 'This article is primary research.'
       #     }
       #   )
-      def self.create(fields = {})
-        citation = Citation.new
-        (Citation.members & fields.keys).each { |member|
-          citation.send(:"#{member}=", fields[member])
-        }
-        citation
+      def initialize(*args)
+        return if !args || args.empty?
+
+        if args.length == 1
+          enumerable = args.first
+          if enumerable.respond_to? :each_pair
+            (MEMBER_ORDER & enumerable.keys).each do |member|
+              self.send(:"#{member}=", enumerable[member])
+            end
+          elsif enumerable.respond_to? :each
+            MEMBER_ORDER.zip(enumerable.each).each do |member, value|
+              self.send(:"#{member}=", value)
+            end
+          end
+        else
+          (MEMBER_ORDER & args).each do |member|
+            self.send(:"#{member}=", hash[member])
+          end
+        end
+      end
+
+      # Returns the +Array+ of +String+ authors.
+      #
+      # @return [Array<String>] array of authors
+      def authors
+        @authors
+      end
+
+      # Sets the authors value.
+      #
+      # @param [#each, #each_pair, #to_s] authors an authors value
+      def authors=(authors)
+        @authors = convert_authors(authors)
       end
 
+      # Returns whether the citation has enough pertinent information to be
+      # considered valid.
+      #
+      # @return [true, false] whether the citation is valid
       def valid?
         type != nil && id != nil && name != nil
       end
+
+      # Returns a +Hash+ of the citation members accoring to #MEMBER_ORDER.
+      #
+      # @return [Hash] citation +Hash+
+      def to_h
+        MEMBER_ORDER.reduce({}) { |hash, member|
+          hash[member] = self.send(member)
+          hash
+        }
+      end
+
+      def to_a
+        MEMBER_ORDER.reduce([]) { |array, member|
+          array << self.send(member)
+          array
+        }
+      end
+
+      private
+
+      def convert_authors(authors)
+        return nil unless authors
+
+        if authors.respond_to? :to_a
+          authors.to_a.map(&:to_s)
+        elsif authors.respond_to? :each
+          @authors = authors.each.to_a.map(&:to_s)
+        elsif authors.respond_to? :to_s
+          authors.to_s.split('|').map(&:strip)
+        else
+          raise ArgumentError.new("authors must be a string-like or iterable")
+        end
+      end
     end
   end
 end