bel_parser 1.0.0.alpha.38 → 1.0.0.alpha.39

data/lib/bel_parser/parsers/expression/term.rl

@@ -3,89 +3,104 @@
 %%{
   machine bel;
 
+  include 'function.rl';
   include 'parameter.rl';
 
-  action start_function {
-    @buffers[:function] = []
-  }
-
-  action append_function {
-    @buffers[:function] << fc
-  }
-
-  action finish_function {
-    @buffers[:function] = identifier(utf8_string(@buffers[:function]))
-  }
-
   action term_init {
+    trace('TERM term_init')
     @buffers[:term_stack] = [ term() ]
   }
 
   action inner_term_init {
+    trace('TERM inner_term_init')
     @buffers[:term_stack] << term()
   }
 
   action term_fx {
-    fx                        = @buffers[:function]
-    @buffers[:term_stack][-1] = @buffers[:term_stack][-1] << function(fx)
+    trace('TERM term_fx')
+    new_term = @buffers[:term_stack][-1] << @buffers[:function]
+    @buffers[:term_stack][-1] = new_term
   }
 
   action term_argument {
-    @buffers[:term_stack][-1] = @buffers[:term_stack][-1] << argument(@buffers[:parameter])
-    @buffers[:parameter]      = nil
+    trace('TERM term_argument')
+    arg_node = argument(@buffers[:parameter])
+    new_term = @buffers[:term_stack][-1] << arg_node
+    @buffers[:term_stack][-1] = new_term
+    @buffers[:parameter] = nil
   }
 
   action fxbt {
-    fpc -= @buffers[:function].length + 1
+    trace('TERM fxbt')
+    function_string = @buffers[:function].identifier.string_literal
+    fpc -= function_string.length + 1
     fcall inner_term;
   }
 
   action fxret {
+    trace('TERM fxret')
     inner_term = @buffers[:term_stack].pop
-    @buffers[:term_stack][-1] = @buffers[:term_stack][-1] << argument(inner_term)
+    arg_node = argument(inner_term)
+    new_term = @buffers[:term_stack][-1] << arg_node
+    @buffers[:term_stack][-1] = new_term
     fret;
   }
 
+  action outer_term_end {
+    trace('TERM outer_term_end')
+    term_stack = @buffers[:term_stack]
+    term_stack.each { |term| term.complete = true }
+  }
+
+  action eof_parameter_argument {
+    trace('TERM eof_parameter_argument')
+    @buffers[:term_stack][-1].complete = false
+    yield @buffers[:term_stack][-1]
+  }
+
   action yield_term_ast  {
     yield @buffers[:term_stack][-1]
   }
 
   inner_term :=
-    IDENT >inner_term_init >start_function $append_function %finish_function
+    a_function >inner_term_init
     SP*
     '(' @term_fx
       (
-        BEL_PARAMETER %term_argument |
-        IDENT >start_function $append_function '(' @fxbt
+        a_parameter %term_argument |
+        a_function '(' @fxbt
       )
       (
-        SP* ',' SP*
+        COMMA_DELIM
         (
-          BEL_PARAMETER %term_argument |
-          IDENT >start_function $append_function '(' @fxbt
+          a_parameter %term_argument |
+          a_function '(' @fxbt
         )
       )*
     ')' @fxret;
 
   outer_term =
-    IDENT >term_init >start_function $append_function %finish_function
+    a_function >term_init
     SP*
     '(' @term_fx
       (
-        BEL_PARAMETER %term_argument |
-        IDENT >start_function $append_function '(' @fxbt
+        a_parameter %term_argument $eof(eof_parameter_argument) |
+        a_function '(' @fxbt
       )
       (
-        SP* ',' SP*
+        COMMA_DELIM
         (
-          BEL_PARAMETER %term_argument |
-          IDENT >start_function $append_function '(' @fxbt
+          a_parameter %term_argument $eof(eof_parameter_argument) |
+          a_function '(' @fxbt
         )
       )*
     ')';
 
   term :=
-    outer_term %yield_term_ast NL;
+    outer_term
+    %outer_term_end
+    %yield_term_ast
+    NL?;
 }%%
 =end
 # end: ragel
@@ -93,6 +108,7 @@
 require_relative '../ast/node'
 require_relative '../mixin/buffer'
 require_relative '../nonblocking_io_wrapper'
+require_relative '../tracer'
 
 module BELParser
   module Parsers
@@ -118,12 +134,13 @@ module BELParser
           include Enumerable
           include BELParser::Parsers::Buffer
           include BELParser::Parsers::AST::Sexp
+          include BELParser::Parsers::Tracer
 
           def initialize(content)
             @content = content
-      # begin: ragel        
+      # begin: ragel
             %% write data;
-      # end: ragel        
+      # end: ragel
           end
 
           def each
@@ -134,10 +151,10 @@ module BELParser
             pe       = data.length
             eof      = data.length
 
-      # begin: ragel        
+      # begin: ragel
             %% write init;
             %% write exec;
-      # end: ragel        
+      # end: ragel
           end
         end
       end

data/lib/bel_parser/parsers/line_parser.rb

@@ -14,6 +14,7 @@ module LINE
     BELParser::Parsers::Common::Identifier,
     BELParser::Parsers::Common::String,
     BELParser::Parsers::Common::List,
+    BELParser::Parsers::Common::Function,
     BELParser::Parsers::Expression::Parameter,
     BELParser::Parsers::Expression::Term,
     BELParser::Parsers::Expression::Relationship,

data/lib/bel_parser/parsers/mixin/buffer.rb

@@ -5,6 +5,10 @@ module BELParser
       def utf8_string(buffer)
         buffer.pack('C*').force_encoding('utf-8')
       end
+
+      def ord_to_str(enumerable)
+      	(enumerable.map { |x| x.chr }).join()
+      end
     end
   end
 end

data/lib/bel_parser/parsers/tracer.rb

@@ -0,0 +1,19 @@
+module BELParser
+  module Parsers
+    # Tracer provides a facility to trace ragel finite state machines.
+    # Tracing is enabled with using +$DEBUG+ or the environment variable
+    # +BELPARSER_PARSER_TRACE+
+    module Tracer
+      # Defines trace on require based on environment.
+      if $DEBUG || (ENV['BELPARSER_PARSER_TRACE'] =~ /^(1|yes|on|true)$/)
+        def trace(msg)
+          $stderr.puts msg
+        end
+      else
+        def trace(_)
+          # no-operation
+        end
+      end
+    end
+  end
+end

data/lib/bel_parser/script/state/namespace_definition.rb

@@ -18,6 +18,7 @@ module BELParser
           resource_reader = script_context[:resource_reader]
 
           keyword, domain = ast_node.children
+          require 'pry'; binding.pry unless domain
           if domain.url?
             prefix  = keyword.identifier.string_literal
             url     = unquote(domain.child.string.string_literal)

metadata

@@ -1,25 +1,25 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.38
+  version: 1.0.0.alpha.39
 platform: ruby
 authors:
 - Anthony Bargnesi
 - Nick Bargnesi
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-05-16 00:00:00.000000000 Z
+date: 2016-05-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
+  name: sparql-client
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 2.0.0
-  name: sparql-client
-  prerelease: false
   type: :runtime
+  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
@@ -303,6 +303,8 @@ files:
 - lib/bel_parser/parsers/common/comment_line.rl
 - lib/bel_parser/parsers/common/common.rb
 - lib/bel_parser/parsers/common/common.rl
+- lib/bel_parser/parsers/common/function.rb
+- lib/bel_parser/parsers/common/function.rl
 - lib/bel_parser/parsers/common/identifier.rb
 - lib/bel_parser/parsers/common/identifier.rl
 - lib/bel_parser/parsers/common/list.rb
@@ -328,6 +330,7 @@ files:
 - lib/bel_parser/parsers/mixin/buffer.rb
 - lib/bel_parser/parsers/nonblocking_io_wrapper.rb
 - lib/bel_parser/parsers/serializer.rb
+- lib/bel_parser/parsers/tracer.rb
 - lib/bel_parser/quoting.rb
 - lib/bel_parser/resource.rb
 - lib/bel_parser/resource/concept.rb
@@ -374,7 +377,7 @@ homepage: https://github.com/OpenBEL/bel_parser
 licenses:
 - Apache-2.0
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -389,9 +392,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: 1.3.1
 requirements: []
-rubyforge_project:
-rubygems_version: 2.6.4
-signing_key:
+rubyforge_project: 
+rubygems_version: 2.5.1
+signing_key: 
 specification_version: 4
 summary: Parser for Biolgical Expression Language.
 test_files: []
+has_rdoc: