bel 0.2.1 → 0.3.0.beta1

data/lib/features.rb

@@ -0,0 +1,21 @@
+# vim: ts=2 sw=2:
+module BEL
+  module Features
+
+    # check for rdf support
+    begin
+      require 'rdf'
+      require 'addressable/uri'
+      require 'uuid'
+      @@rdf_support = true
+    rescue LoadError => e
+      # exceptional condition; missing non-optional or downstream deps
+      @@rdf_support = false
+      raise unless e.message =~ /rdf/ or e.message =~ /addressable/
+    end
+
+    def self.rdf_support?
+      @@rdf_support
+    end
+  end
+end

data/lib/libbel.rb

@@ -0,0 +1,201 @@
+module LibBEL
+
+  class << self
+
+    def rubinius?
+      defined?(RUBY_ENGINE) && ("rbx" == RUBY_ENGINE)
+    end
+
+    # @api_private
+    # Determine FFI constant for this ruby engine.
+    def find_ffi
+      if rubinius?
+        # Use ffi gem instead of rubinius-bundled FFI
+        # Rubinius 2.5.2 does not seem to support FFI::ManagedStruct
+        require "ffi"
+        ::FFI
+      else # mri, jruby, etc
+        require "ffi"
+        ::FFI
+      end
+    end
+
+    # @api_private
+    # Extend with the correct ffi implementation.
+    def load_ffi
+      ffi_module = LibBEL::find_ffi
+      extend ffi_module::Library
+      ffi_module
+    end
+
+    # @api_private
+    # Loads the libkyotocabinet shared library.
+    def load_libBEL
+      ffi_module = find_ffi
+      extend ffi_module::Library
+
+      # libbel.so:     Linux and MinGW
+      # libbel.bundle: Mac OSX
+      messages = []
+      library_loaded = ['libbel.so', 'libbel.bundle'].map { |library_file|
+        File.join(
+          File.expand_path(File.dirname(__FILE__)),
+          library_file
+        )
+      }.any? do |library_path|
+        begin
+          ffi_lib library_path
+          true
+        rescue LoadError => exception
+          messages << exception.to_s
+          false
+        end
+      end
+
+      if !library_loaded
+        msg = messages.map { |msg| "  #{msg}" }.join("\n")
+        fail LoadError.new("Failed to load libbel library. Details:\n#{msg}")
+      end
+    end
+  end
+
+  # Constant holding the FFI module for this ruby engine.
+  FFI = LibBEL::load_ffi
+  LibBEL::load_libBEL
+
+  # typedef enum bel_token_type
+  enum :bel_token_type, [
+    :IDENT,   0,
+    :STRING,
+    :O_PAREN,
+    :C_PAREN,
+    :COLON,
+    :COMMA,
+    :SPACES
+  ]
+
+  class BelToken < FFI::Struct
+
+    layout :type,      :bel_token_type,
+           :pos_start, :int,
+           :pos_end,   :int,
+           :value,     :pointer
+
+    def type
+      self[:type]
+    end
+
+    def pos_start
+      self[:pos_start]
+    end
+
+    def pos_end
+      self[:pos_end]
+    end
+
+    def value
+      self[:value].read_string
+    end
+
+    def hash
+      [self.type, self.value, self.pos_start, self.pos_end].hash
+    end
+
+    def ==(other)
+      return false if other == nil
+      self.type == other.type && self.value == other.value &&
+        self.pos_start == other.pos_start && self.pos_end == other.pos_end
+    end
+
+    alias_method :eql?, :'=='
+  end
+
+  class BelTokenList < FFI::ManagedStruct
+    include Enumerable
+
+    layout :length,    :int,
+           :tokens,    BelToken.ptr
+
+    def each
+      if block_given?
+        iterator = LibBEL::bel_new_token_iterator(self.pointer)
+        while LibBEL::bel_token_iterator_end(iterator).zero?
+          current_token = LibBEL::bel_token_iterator_get(iterator)
+          yield LibBEL::BelToken.new(current_token)
+          LibBEL::bel_token_iterator_next(iterator)
+        end
+        LibBEL::free_bel_token_iterator(iterator)
+      else
+        enum_for(:each)
+      end
+    end
+
+    def token_at(position)
+      self.each_with_index { |tk, index|
+        if (tk.pos_start..tk.pos_end).include? position
+          return [tk, index]
+        end
+      }
+      nil
+    end
+
+    def self.release(ptr)
+      LibBEL::free_bel_token_list(ptr)
+    end
+  end
+
+  class BelTokenIterator < FFI::ManagedStruct
+    include Enumerable
+
+    layout :index,         :int,
+           :list,          :pointer,
+           :current_token, :pointer
+
+    def each
+      if self.null? or not LibBEL::bel_token_iterator_end(self).zero?
+        fail StopIteration, "bel_token_iterator reached end"
+      end
+
+      if block_given?
+        while LibBEL::bel_token_iterator_end(self.pointer).zero?
+          current_token = LibBEL::bel_token_iterator_get(self.pointer)
+          yield LibBEL::BelToken.new(current_token)
+          LibBEL::bel_token_iterator_next(self.pointer)
+        end
+      else
+        enum_for(:each)
+      end
+    end
+
+    def self.release(ptr)
+      LibBEL::free_bel_token_iterator(ptr)
+    end
+  end
+
+  attach_function :bel_new_token,           [:bel_token_type, :pointer, :pointer, :pointer], :pointer
+  attach_function :bel_new_token_list,      [:int                                         ], :pointer
+  attach_function :bel_new_token_iterator,  [:pointer                                     ], :pointer
+  attach_function :bel_token_iterator_get,  [:pointer                                     ], :pointer
+  attach_function :bel_token_iterator_next, [:pointer                                     ], :void
+  attach_function :bel_token_iterator_end,  [:pointer                                     ], :int
+  attach_function :bel_parse_term,          [:string                                      ], :pointer
+  attach_function :bel_tokenize_term,       [:string                                      ], :pointer
+  attach_function :bel_print_token,         [:pointer                                     ], :void
+  attach_function :bel_print_token_list,    [:pointer                                     ], :void
+  attach_function :free_bel_token,          [:pointer                                     ], :void
+  attach_function :free_bel_token_list,     [:pointer                                     ], :void
+  attach_function :free_bel_token_iterator, [:pointer                                     ], :void
+
+  def self.tokenize_term(string)
+    LibBEL::BelTokenList.new(self.bel_tokenize_term(string))
+  end
+
+  def self.print_token(token)
+    self.bel_print_token(token.pointer)
+  end
+
+  def self.print_token_list(list)
+    self.bel_print_token_list(list.pointer)
+  end
+end
+

data/lib/util.rb

@@ -0,0 +1,125 @@
+require 'digest'
+require 'open-uri'
+require 'pathname'
+require 'tempfile'
+
+module BEL
+
+  def self.read_all(reference)
+    if self.cached? reference
+      self.read_cached reference do |cf|
+        return cf.read
+      end
+    end
+
+    self.multi_open(reference) do |f|
+      content = f.read
+      self.write_cached reference, content
+      return content
+    end
+  end
+
+  def self.read_lines(reference)
+    if self.cached? reference
+      self.read_cached reference do |cf|
+        return cf.readlines
+      end
+    end
+
+    self.multi_open(reference) do |f|
+      content = f.read
+      self.write_cached reference, content
+      f.rewind
+      return f.readlines
+    end
+  end
+
+  private
+
+  def self.multi_open(reference)
+    if self.cached? reference
+      self.read_cached reference do |cf|
+        if block_given?
+          yield cf
+        else
+          return cf
+        end
+      end
+      return
+    end
+
+    if File.exists? reference
+      File.open(reference) do |f|
+        if block_given?
+          yield f
+        else
+          return f
+        end
+      end
+    elsif reference.start_with? 'file:'
+      File.open(URI(reference).path) do |f|
+        if block_given?
+          yield f
+        else
+          return f
+        end
+      end
+    else
+      open(reference) do |f|
+        if block_given?
+          yield f
+        else
+          return f
+        end
+      end
+    end
+  end
+
+  def self.cached?(identifier, options = {})
+    options = {
+      temp_dir: Dir::tmpdir
+    }.merge(options)
+    cached_name = cached_filename_for identifier
+    path = Pathname(options[:temp_dir]) + cached_name
+    File.exist? path
+  end
+
+  def self.read_cached(identifier, options = {})
+    options = {
+      temp_dir: Dir::tmpdir
+    }.merge(options)
+    cached_name = cached_filename_for identifier
+    path = Pathname(options[:temp_dir]) + cached_name
+    File.open(path, "r") do |f|
+      if block_given?
+        yield f
+      else
+        return f.read
+      end
+    end
+    path.to_s
+  end
+
+  def self.write_cached(identifier, data = '', options = {})
+    options = {
+      temp_dir: Dir::tmpdir
+    }.merge(options)
+    cached_name = cached_filename_for identifier
+    path = Pathname(options[:temp_dir]) + cached_name
+    File.open(path, "w") do |f|
+      if block_given?
+        yield f
+      else
+        f.write(data)
+      end
+    end
+    path.to_s
+  end
+
+  def self.cached_filename_for(identifier)
+    return nil unless identifier
+    "#{self.to_s}_#{Digest::SHA256.hexdigest identifier}"
+  end
+end
+# vim: ts=2 sw=2
+# encoding: utf-8

metadata

@@ -1,123 +1,270 @@
 --- !ruby/object:Gem::Specification
 name: bel
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.3.0.beta1
+  prerelease: 6
 platform: ruby
 authors:
 - Anthony Bargnesi
+- Natalie Catlett
+- Nick Bargnesi
+- William Hayes
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-01-13 00:00:00.000000000 Z
+date: 2015-03-14 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: ffi
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.9'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.9'
+- !ruby/object:Gem::Dependency
+  name: uuid
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.3'
+- !ruby/object:Gem::Dependency
+  name: addressable
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.3'
+- !ruby/object:Gem::Dependency
+  name: rdf
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.1'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.1'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.7'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '10.1'
+        version: '10.4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '10.1'
+        version: '10.4'
 - !ruby/object:Gem::Dependency
-  name: rspec
+  name: rake-compiler
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '2.14'
+        version: '0.9'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '2.14'
+        version: '0.9'
 - !ruby/object:Gem::Dependency
-  name: yard
+  name: rspec
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0.8'
+        version: '3.2'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0.8'
+        version: '3.2'
 - !ruby/object:Gem::Dependency
-  name: rdoc
+  name: yard
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '4.0'
+        version: '0.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '4.0'
+        version: '0.8'
 - !ruby/object:Gem::Dependency
-  name: bundler
+  name: rdoc
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: '4.2'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '1.3'
-description: The BEL gem allows the reading, writing, and processing of BEL (Biological
-  Expression Language) with a natural DSL.
-email: abargnesi@selventa.com
+        version: '4.2'
+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
+- nbargnesi@selventa.com
+- whayes@selventa.com
 executables:
+- bel_summarize
+- bel_rdfschema
+- bel_upgrade_term
+- bel2rdf
+- bel_parse
+- bel_compare
 - bel_upgrade
-extensions: []
+extensions:
+- ext/mri/extconf.rb
 extra_rdoc_files: []
 files:
-- LICENSE
-- bin/bel_upgrade
-- lib/bel.rb
+- lib/util.rb
+- lib/libbel.rb
+- lib/bel/quoting.rb
+- lib/bel/rdf.rb
+- lib/bel/completion.rb
+- lib/bel/completion_rule.rb
+- lib/bel/script.rb
 - lib/bel/language.rb
 - lib/bel/namespace.rb
-- lib/bel/parse_objects.rb
-- lib/bel/script.rb
+- lib/features.rb
+- lib/bel.rb
+- ext/mri/bel-token.c
+- ext/mri/bel-ast.c
+- ext/mri/bel-tokenize-term.c
+- ext/mri/libbel.c
+- ext/mri/bel-parser.c
+- ext/mri/bel-parse-statement.c
+- ext/mri/bel-parse-term.c
+- ext/mri/bel-node-stack.c
+- ext/mri/bel-token.h
+- ext/mri/bel-node-stack.h
+- ext/mri/bel-parser.h
+- ext/mri/bel-ast.h
+- ext/mri/libbel.def
+- bel.gemspec
+- LICENSE
+- INSTALL.md
+- INSTALL_RUBY.md
+- README.md
+- bin/bel_summarize
+- bin/bel_rdfschema
+- bin/bel_upgrade_term
+- bin/bel2rdf
+- bin/bel_parse
+- bin/bel_compare
+- bin/bel_upgrade
+- ext/mri/extconf.rb
 homepage: https://github.com/OpenBEL/bel.rb
 licenses:
 - Apache-2.0
-metadata: {}
 post_install_message: 
-rdoc_options: []
+rdoc_options:
+- --title
+- BEL Ruby Documentation
+- --main
+- README.md
+- --line-numbers
+- --exclude
+- lib/bel/script.rb
+- README.md
+- INSTALL.md
+- INSTALL_RUBY.md
+- LICENSE
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.9.2
 required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>'
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.0
+rubygems_version: 1.8.23.2
 signing_key: 
-specification_version: 4
+specification_version: 3
 summary: Process BEL with ruby.
 test_files: []
 has_rdoc: