bel_parser 1.0.0.alpha.15 → 1.0.0.alpha.16

checksums.yaml

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

@@ -4,6 +4,17 @@ Parser for BEL expressions and the BEL Script document format.
 
 ### Installation
 
+  gem install bel_parser --pre
+
 ### Getting Started
 
+Two tools are available to try out:
+1) bel_script_reader - will read a BEL Script with a specified BEL version and not any warning or errors with the script
+
+2) bel2_validator - will read in lines and validate the BEL Statements
+
+Example script using bel_parser module
+
+  examples/upgrade_kinase.rb
+
 ### Design

data/VERSION

@@ -1 +1 @@
-1.0.0.alpha.15
+1.0.0.alpha.16

data/bin/bel_script_reader

@@ -2,27 +2,51 @@
 $LOAD_PATH.unshift(
   File.join(File.expand_path(File.dirname(__FILE__)), '..', 'lib'))
 
-bel_specification_version, file = ARGV
+require 'optparse'
+require 'bel_parser'
+require 'bel_parser/resource/resource_file_reader'
+
+options = {
+  spec: BELParser::Language.specification(
+    BELParser::Language.latest_supported_version)
+}
+OptionParser.new do |opts|
+  opts.banner = <<-USAGE.gsub(/^ {4}/, '')
+    Validates BEL Script with support for multiple BEL specifications.
+
+    Read from a BEL file.
+    usage: #$PROGRAM_NAME --file [FILE]
 
-unless bel_specification_version
-  program = File.basename($PROGRAM_NAME)
-  $stderr.puts <<-USAGE.gsub(/ {4}/, '')
-    usage: #{program} [BEL specification version]
+    Read from standard input.
+    usage: #$PROGRAM_NAME
   USAGE
-  exit 1
-end
 
+  opts.on('-f', '--file FILE', 'BEL script file to read.') do |bel|
+    options[:file] = bel
+  end
+
+  opts.on(
+    '-s',
+    '--specification VERSION',
+    'BEL specification version (e.g. 1.0, 2.0)') do |spec|
+
+    unless BELParser::Language.defines_version?(spec)
+      $stderr.puts %(Invalid BEL specification "#{spec}")
+      exit 1
+    end
+
+    options[:spec] = BELParser::Language.specification(spec)
+  end
+end.parse!
+
+file, spec = options.values_at(:file, :spec)
 io =
   if file
-    File.open(ARGV.first, external_encoding: 'UTF-8')
+    File.open(file, external_encoding: 'UTF-8')
   else
     $stdin
   end
 
-require 'bel_parser/language'
-require 'bel_parser/script/validator'
-require 'bel_parser/resource/resource_file_reader'
-
 def select(list, cls)
   list.select { |item| item.is_a?(cls) }
 end
@@ -46,11 +70,19 @@ SYN_ERR  = BELParser::Language::Syntax::SyntaxError
 SYN_WARN = BELParser::Language::Syntax::SyntaxWarning
 SEM_WARN = BELParser::Language::Semantics::SemanticsWarning
 
+rr         = BELParser::Resource::ResourceFileReader.new
+namespaces = Hash[
+  ARGV.map do |ns|
+    prefix, identifier = ns.split('=')
+    dataset            = rr.retrieve_resource(identifier)
+    dataset ? [prefix, dataset] : nil
+  end.compact
+]
+
 initial_state = {
-  resource_reader: BELParser::Resource::ResourceFileReader.new,
-  specification:   BELParser::Language.specification(
-    bel_specification_version
-  )
+  resource_reader:       BELParser::Resource::ResourceFileReader.new,
+  specification:         spec,
+  namespace_definitions: namespaces
 }
 
 BELParser::Script::Validator

data/lib/bel_parser/language/expression_validator.rb

@@ -10,7 +10,7 @@ module BELParser
     class ExpressionValidator
       def initialize(spec, namespaces, resource_reader)
         @spec                = spec
-        @namespaces          = namespaces
+        @namespaces          = namespaces || {}
         @syntax_functions    = Syntax.syntax_functions
         @semantics_functions = Semantics.semantics_functions
         @transform           =

data/lib/bel_parser/language/semantics_ast.rb

@@ -670,8 +670,13 @@ module BELParser
         def match(identifier, spec)
           return success(identifier, spec) if return_types.include?(:*)
 
-          fxret = spec.function(identifier.string_literal.to_sym).return_type
-          if return_types.any? { |rt| fxret <= rt }
+          function = spec.function(identifier.string_literal.to_sym)
+          return invalid_return_type_warning(
+            identifier,
+            spec,
+            return_types) unless function
+
+          if return_types.any? { |rt| function.return_type <= rt }
             success(identifier, spec)
           else
             invalid_return_type_warning(identifier, spec, return_types)

data/lib/bel_parser/language/syntax/undefined_namespace_value.rb

@@ -1,4 +1,5 @@
 require 'bel_parser/parsers/ast/node'
+require 'bel_parser/quoting'
 
 module BELParser
   module Language
@@ -6,6 +7,7 @@ module BELParser
       # Undefined namespace value finds values that are missing from their
       # purported namespaces.
       class UndefinedNamespaceValue
+        extend BELParser::Quoting
         include SyntaxFunction
 
         private_class_method :new
@@ -15,7 +17,7 @@ module BELParser
           return nil unless value_node.namespace
 
           unless value_node.namespace_value
-            value = value_node.children[0].string_literal
+            value = unquote(value_node.children[0].string_literal)
             UndefinedNamespaceValueWarning.new(value_node, spec, value)
           end
         end

data/lib/bel_parser/script/keywords.rb

@@ -0,0 +1,12 @@
+module BELParser
+  module Script
+    module Keyword
+      BEL_VERSION_STRING = 'BELVersion'.freeze
+      BEL_VERSION_REGEX  = /\A#{BEL_VERSION_STRING}\Z/i
+
+      def is_bel_version?(string)
+        string.to_s.strip =~ BEL_VERSION_REGEX
+      end
+    end
+  end
+end

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

@@ -2,6 +2,7 @@ require 'bel_parser/language'
 require 'bel_parser/parsers/ast/node'
 require 'bel_parser/quoting'
 require 'concurrent/hash'
+require_relative '../keywords'
 require_relative '../state_function'
 
 module BELParser
@@ -10,16 +11,16 @@ module BELParser
       class BELVersion
         extend StateFunction
         extend BELParser::Quoting
+        extend Keyword
 
         TARGET_NODE         = BELParser::Parsers::AST::DocumentProperty
-        BEL_VERSION_REGEX   = /#{Regexp.escape('bel_version')}/i
         DEFAULT_BEL_VERSION = '2.0'
 
         def self.consume(ast_node, script_context)
           return unless ast_node.is_a?(TARGET_NODE)
           name, value = ast_node.children
           name_string  = name.identifier.string_literal
-          return unless name_string =~ BEL_VERSION_REGEX
+          return unless is_bel_version?(name_string)
 
           value_string = unquote(value.children[0].string_literal)
           begin

data/lib/bel_parser/script/syntax/unsupported_bel_version.rb

@@ -4,6 +4,7 @@ require 'bel_parser/language/syntax_error'
 require 'bel_parser/quoting'
 require 'bel_parser/parsers/ast/node'
 require 'concurrent/hash'
+require_relative '../keywords'
 
 module BELParser
   module Script
@@ -11,15 +12,15 @@ module BELParser
       class UnsupportedBELVersion
         extend BELParser::Language::Syntax::SyntaxFunction
         extend BELParser::Quoting
+        extend Keyword
 
         TARGET_NODE         = BELParser::Parsers::AST::DocumentProperty
-        BEL_VERSION_REGEX   = /#{Regexp.escape('bel_version')}/i
 
         def self.map(ast_node, script_context)
           return nil unless ast_node.is_a?(TARGET_NODE)
           name, value = ast_node.children
           name_string  = name.identifier.string_literal
-          return nil unless name_string =~ BEL_VERSION_REGEX
+          return nil unless is_bel_version?(name_string)
 
           value_string = unquote(value.children[0].string_literal)
           begin

data/lib/bel_parser/script.rb

@@ -0,0 +1,5 @@
+require_relative 'script/keywords'
+require_relative 'script/state_function'
+
+require_relative 'script/parser'
+require_relative 'script/validator'

data/lib/bel_parser.rb

@@ -15,3 +15,6 @@ require 'bel_parser/ast_filter'
 
 # Language; version-independent classes
 require 'bel_parser/language'
+
+# BEL Script support
+require 'bel_parser/script'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.15
+  version: 1.0.0.alpha.16
 platform: ruby
 authors:
 - Anthony Bargnesi
@@ -312,6 +312,8 @@ files:
 - lib/bel_parser/resource/resource_file_reader.rb
 - lib/bel_parser/resource/sparql_reader.rb
 - lib/bel_parser/resource/value.rb
+- lib/bel_parser/script.rb
+- lib/bel_parser/script/keywords.rb
 - lib/bel_parser/script/parser.rb
 - lib/bel_parser/script/state/annotation_definition.rb
 - lib/bel_parser/script/state/bel_version.rb