bel_parser 1.0.5-java → 1.0.6-java

checksums.yaml

@@ -1,7 +1,7 @@
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data/{.gemspec-java → .gemspec}

@@ -5,6 +5,7 @@ Gem::Specification.new do |spec|
                                    File.expand_path(File.dirname(__FILE__)),
                                    'VERSION'))
   spec.summary               = %q{Parser for Biolgical Expression Language.}
+  spec.platform              = 'java'
   spec.description           = %q{Implements language versions 1.0 and 2.0.}
   spec.license               = 'Apache-2.0'
   spec.authors               = [
@@ -26,8 +27,5 @@ Gem::Specification.new do |spec|
   spec.require_paths         = ['lib']
   spec.required_ruby_version = '>= 2.0.0'
 
-  spec.platform              = 'java'
   spec.add_runtime_dependency  'sparql-client', '~> 2.0.0'
-  spec.add_runtime_dependency  'dbm-mapdb3',    '~> 0.6.0.beta'
 end
-# vim: ft=ruby

data/README.md

@@ -1,20 +1,73 @@
 # bel_parser
 
-Parser for BEL expressions and the BEL Script document format.
+The bel_parser gem implements BEL specifications (currently 1.0 and 2.0) and BEL Script nanopub format.
 
 ### Installation
 
-  gem install bel_parser --pre
+  gem install bel_parser
+
+### Motivation
+
+The motivation for this library is to provide the building blocks to implement BEL specifications more easily. This includes:
+
+- Recognizing input to Abstract Syntax Trees
+- Applying syntax validation relative to a BEL specification.
+- Applying signature validation relative to a BEL specification.
+- Conversion of Abstract Syntax Trees to a Nanopub object model.
+
+Currently BEL 1.0 and 2.0 specifications are implemented.
 
 ### 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
+bel_parser provides a Ruby library and a set of command-line tools.
+
+Command-line tools:
+
+1. *bel2_debug_ast*
+
+  Writes the AST output recognized from the input.
+
+  usage: `bel2_debug_ast` (Then enter a line at a time)
+
+  usage: `bel2_debug_ast --file file.bel`
+
+2. *bel2_validator*
+
+  Validate the syntax and semantics of the AST recognized from the input.
+
+  usage: `bel2_validator` (Then enter a line at a time)
+
+  usage: `bel2_validator --file file.bel --specification 2.0`
+
+3. *bel2_upgrade*
+
+  Upgrades BEL statements from 1.0 to 2.0.
+
+  usage: `bel2_upgrade` (Then enter a line at a time)
+
+  usage: `bel2_upgrade --file file.bel`
+
+### Development / Deployment
+
+Development for the next release should be performed on the *next* branch. When the new changes are complete, functional, and tested they should be merged over to the *master* branch.
+
+To make a release, perform the following steps:
+
+- Update the version in the `VERSION` file.
+
+- Add a new version with list of changes in the `CHANGELOG` file. This file is modelled after http://keepachangelog.com/.
+
+- Build the Ruby and Java versions of the gem:
+
+  Ruby: `gem build .gemspec`
+
+  Java: `gem build .gemspec-java`
+
+- Create a release on GitHub with both gems and a summary of the changes in this version.
 
-2) bel2_validator - will read in lines and validate the BEL Statements
+- Push both gems to RubyGems:
 
-Example script using bel_parser module
+  `gem push bel_parser-VERSION.gem`
 
-  examples/upgrade_kinase.rb
+  `gem push bel_parser-VERSION-java.gem`
 
-### Design

data/VERSION

@@ -1 +1 @@
-1.0.5
+1.0.6

data/lib/bel/translator/plugins/bel_script/nanopub_serialization.rb

@@ -1,11 +1,11 @@
-require 'bel/quoting'
+require 'bel_parser/quoting'
 
 # Serializing of common {BEL::Nanopub::Nanopub nanopub} components to BEL
 # Script syntax.
 #
 # @abstract
 module BEL::Translator::Plugins::BelScript::NanopubSerialization
-  include BEL::Quoting
+  include BELParser::Quoting
 
   # Serialize the {BEL::Nanopub::Nanopub nanopub} to a BEL Script string.
   #
@@ -32,11 +32,13 @@ module BEL::Translator::Plugins::BelScript::NanopubSerialization
 
     values = citation.to_a
     values.map! { |v|
-      v ||= ""
+      v = %("") if v.nil? || v.empty?
       if v.respond_to?(:each)
-        %Q{"#{v.join('|')}"}
+        v.map! { |item| item.delete("\r\n") }
+        quote(v.join('|'))
       else
-        %Q{"#{v}"}
+        v.delete!("\r\n")
+        quote(v)
       end
     }
     values.join(', ')

data/lib/bel/translator/plugins/bel_script/writer.rb

@@ -45,7 +45,7 @@ module BEL::Translator::Plugins
             }
             serialization_module = serialization_refs[serialization.to_sym]
             unless serialization_module
-                raise %Q{No BEL serialization strategy for "#{serialization}"}
+                raise %(No BEL serialization strategy for "#{serialization}")
             end
             serialization_module
           else
@@ -81,7 +81,7 @@ module BEL::Translator::Plugins
             bel = to_bel(nanopub)
 
             if @write_header && header_flag
-              yield document_header(nanopub.metadata.document_header)
+              yield document_header(nanopub.metadata)
               yield namespaces(combiner.namespace_references)
               yield annotations(combiner.annotation_references)
 
@@ -103,30 +103,35 @@ module BEL::Translator::Plugins
 
       private
 
-      def document_header(header)
-        return "" unless header
-
+      def document_header(metadata)
         bel = <<-COMMENT.gsub(/^\s+/, '')
           ###############################################
           # Document Properties Section
         COMMENT
 
-        header.each { |name, value|
-          name_s  = name.to_s
-          value_s =
-            if value.respond_to?(:each)
-              value.join('|')
-            else
-              value.to_s
-            end
-
-          # handle casing for document properties (special case, contactinfo)
-          name_s = (name_s.downcase == 'contactinfo') ?
-            'ContactInfo' :
-            name_s.capitalize
-
-          bel << %Q{SET DOCUMENT #{name_s} = "#{value_s}"\n}
-        }
+        bel_version =
+          metadata.bel_version || BELParser::Language.default_version
+        bel << %(SET DOCUMENT BELVersion = "#{bel_version}"\n)
+
+        if metadata.document_header
+          header = metadata.document_header
+          header.each do |name, value|
+            name_s  = name.to_s
+            value_s =
+              if value.respond_to?(:each)
+                value.join('|')
+              else
+                value.to_s
+              end
+
+            # handle casing for document properties (special case, contactinfo)
+            name_s = (name_s.downcase == 'contactinfo') ?
+              'ContactInfo' :
+              name_s.capitalize
+
+            bel << %(SET DOCUMENT #{name_s} = "#{value_s}"\n)
+          end
+        end
 
         bel << "\n"
         bel
@@ -145,14 +150,14 @@ module BEL::Translator::Plugins
 
           case ref.type.to_sym
           when :url
-            bel << %Q{URL "#{ref.domain}"\n}
+            bel << %(URL "#{ref.domain}"\n)
           when :uri
-            bel << %Q{URI "#{ref.domain}"\n}
+            bel << %(URI "#{ref.domain}"\n)
           when :pattern
             regex = ref.domain.respond_to?(:source) ? ref.domain.source : ref.domain
-            bel << %Q{PATTERN "#{regex}"\n}
+            bel << %(PATTERN "#{regex}"\n)
           when :list
-            bel << %Q|LIST {#{ref.domain.inspect[1...-1]}}\n|
+            bel << %(LIST {#{ref.domain.inspect[1...-1]}}\n)
           end
           bel
         }
@@ -169,7 +174,13 @@ module BEL::Translator::Plugins
         return bel unless namespace_references
 
         namespace_references.reduce(bel) { |bel, ref|
-          bel << %Q{DEFINE NAMESPACE #{ref.keyword} AS URL "#{ref.uri}"\n}
+          case
+          when ref.uri?
+            bel << %(DEFINE NAMESPACE #{ref.keyword} AS URI "#{ref.uri}"\n)
+          when ref.url?
+            bel << %(DEFINE NAMESPACE #{ref.keyword} AS URL "#{ref.url}"\n)
+          end
+
           bel
         }
         bel << "\n"

data/lib/bel_parser/expression/model/annotation.rb

@@ -20,8 +20,13 @@ module BELParser
           @type    = type.to_sym
           @domain  = domain
 
-          uri_reader = options.fetch(:uri_reader, nil)
-          url_reader = options.fetch(:url_reader, nil)
+          # configure reader for URIs (RDF).
+          @uri_reader = options.fetch(:uri_reader, BELParser::Resource.default_uri_reader)
+          BELParser::Resource::Reader.assert_reader(@uri_reader, 'uri_reader')
+
+          # configure reader for URLs (Resource files).
+          @url_reader = options.fetch(:url_reader, BELParser::Resource.default_url_reader)
+          BELParser::Resource::Reader.assert_reader(@url_reader, 'url_reader')
         end
 
         def initialize_copy(original)

data/lib/bel_parser/expression/model/statement.rb

@@ -16,7 +16,7 @@ module BELParser
       # - SUBJECT RELATIONSHIP OBJECT(Statement)
       #   - +p(HGNC:VHL) -> (p(HGNC:TNF) -> bp(GOBP:"cell death"))+
       class Statement
-        attr_accessor :subject, :relationship, :object, :comment
+        attr_reader :subject, :relationship, :object, :comment, :type
 
         # Creates a {Statement} with +subject+, +relationship+, +object+, and
         # +comment+.
@@ -33,44 +33,58 @@ module BELParser
           end
           @subject = subject
 
-          unless relationship.nil? || relationship.is_a?(BELParser::Language::Relationship)
-            raise(
-              ArgumentError,
+          case relationship
+          when nil
+            @type         = :observed_term
+            @relationship = nil
+          when BELParser::Language::Relationship
+            @type         = :simple_statement
+            @relationship = relationship
+          else
+            raise(ArgumentError,
               "relationship: expected nil or Relationship, actual #{relationship.class}")
           end
-          @relationship = relationship
 
-          unless object.nil? || [Term, Statement].any?(&object.method(:is_a?))
-            raise(
-              ArgumentError,
+          case object
+          when nil
+            @type   = :observed_term
+            @object = nil
+          when BELParser::Expression::Model::Term
+            @type   = :simple_statement
+            @object = object
+          when BELParser::Expression::Model::Statement
+            @type   = :nested_statement
+            @object = object
+          else
+            raise(ArgumentError,
               "object: expected nil, Term, or Statement, actual #{object.class}")
           end
-          @object       = object
-          @comment      = comment
 
-          if @relationship && !@object
+          @comment = comment
+
+          if @relationship && @object.nil?
             raise(
               ArgumentError,
               "object must be set when specifying a relationship")
           end
 
-          if @object && !@relationship
+          if @object && @relationship.nil?
             raise(
               ArgumentError,
-              "relationsihp must be set when specifying an object")
+              "relationship must be set when specifying an object")
           end
         end
 
         def subject_only?
-          !@relationship
+          @type == :observed_term
         end
 
         def simple?
-          @object && @object.is_a?(Term)
+          @type == :simple_statement
         end
 
         def nested?
-          @object && @object.is_a?(Statement)
+          @type == :nested_statement
         end
 
         def namespaces

data/lib/bel_parser/language/function.rb

@@ -41,9 +41,7 @@ module BELParser
       end
 
       def to_sym(form = :short)
-        value = _form_value(form)
-        return nil unless value
-        value.to_s
+        _form_value(form)
       end
 
       def to_s(form = :short)

data/lib/bel_parser/language/relationship.rb

@@ -76,9 +76,7 @@ module BELParser
       end
 
       def to_sym(form = :short)
-        value = _form_value(form)
-        return nil unless value
-        value.to_s
+        _form_value(form)
       end
 
       def to_s(form = :short)

data/lib/bel_parser/mixin/line_mapping.rb

@@ -3,7 +3,7 @@ module BELParser
   module LineMapping
     def normalize_line_terminator(line)
       return nil unless line
-      line.sub(/[\r\n]+$/, '') + "\n"
+      "#{line.chomp}\n"
     end
 
     def map_lines(line_enumerator)

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

@@ -60,7 +60,12 @@ module BELParser
         def self.handle_annotation(name_string, value_node, script_context)
           # add to annotation state
           script_context[:annotations]              ||= Concurrent::Hash.new
-          script_context[:annotations][name_string]   = value_node.children[0].string_literal
+          if value_node.children[0].respond_to?(:string_literal)
+              namestr = value_node.children[0].string_literal
+          else
+              namestr = value_node.children[0].to_s
+          end
+          script_context[:annotations][name_string]   = namestr
         end
         private_class_method :handle_annotation
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.5
+  version: 1.0.6
 platform: java
 authors:
 - Anthony Bargnesi
@@ -25,32 +25,18 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 2.0.0
-- !ruby/object:Gem::Dependency
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 0.6.0.beta
-  name: dbm-mapdb3
-  prerelease: false
-  type: :runtime
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 0.6.0.beta
 description: Implements language versions 1.0 and 2.0.
 email: abargnesi@selventa.com
 executables:
-- bel2_upgrade
-- bel2_debug_ast
-- bel2_validator
-- bel_script_reader
 - bel2_compatibility
+- bel_script_reader
+- bel2_validator
+- bel2_debug_ast
+- bel2_upgrade
 extensions: []
 extra_rdoc_files: []
 files:
-- ".gemspec-java"
+- ".gemspec"
 - CHANGELOG.md
 - LICENSE
 - README.md