bel_parser 1.0.0.alpha.21 → 1.0.0.alpha.22

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 84bb8cded6070abe5f02e93703c149cbb3adfd88
+  metadata.gz: 2e418c5b2fae45c7d2d04f8d6f6192fff2f1f1d4
+  data.tar.gz: 42a84936274b3cdd6eccdb2918b2b5ad37f49551
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+  metadata.gz: 356b39aebd42b4298a29d2a4e7ec1521855a5def19f6c1baa8b5769c81a14866f3bab2f7c28450171682b41bb841f47b11c3cd6a98c05ff52749dff53bc294b4
+  data.tar.gz: f9f900d99b8ba8f5adfd72d5a08747a2b3771bee8a475fa0e2408712ac5ae1cc9470eb49d40837687bc83b6ca4b8e2ea31a4b2174ee627dc5fdb69ce18458d26

data/VERSION

@@ -1 +1 @@
-1.0.0.alpha.21
+1.0.0.alpha.22

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

@@ -6,8 +6,10 @@ module BEL::Translator::Plugins
   module BelScript
     class Reader
       include ::BELParser::Script
+      
+      SyntaxError = ::BELParser::Language::Syntax::SyntaxError
 
-      def initialize(io)
+      def initialize(io, options = {})
         @io    = io
         @state = {
           resource_reader: BELParser::Resource::ResourceURLReader.new(true),
@@ -22,8 +24,11 @@ module BEL::Translator::Plugins
             Validator.new(
               StateAggregator.new(
                 FirstNode.new(Filter.new(BELParser::ASTGenerator.new(@io))),
-                @state))).each do |hash|
-                  yield ::BEL::Model::Evidence.create(hash)
+                @state)),
+            true,
+            false
+          ).each do |(num, line, ast_node, nanopub_hash)|
+                  yield ::BEL::Model::Evidence.create(nanopub_hash)
                 end
         else
           enum_for(:each)

data/lib/bel_parser/script/nanopub_mapper.rb

@@ -17,22 +17,35 @@ module BELParser
 
       DEFINITIONS = [:annotation_definitions, :namespace_definitions]
 
-      def initialize(ast_enum)
-        @ast_enum = ast_enum
+      def initialize(ast_enum, omit_on_error = false, omit_on_warning = false)
+        @ast_enum        = ast_enum
+        @omit_on_error   = omit_on_error
+        @omit_on_warning = omit_on_warning
       end
 
-      def each(&block)
+      def each
         if block_given?
-          @ast_enum.each do |(line_nunber, line, ast_node, state)|
+          @ast_enum.each do |(num, line, ast_node, state)|
             next unless STATEMENT_TYPES.include?(ast_node.type)
-            yield nanopub(ast_node, state, &block)
+
+            errors   = errors(ast_node)
+            warnings = warnings(ast_node)
+
+            if (@omit_on_error && !errors.empty?) ||
+              (@omit_on_warning && !warnings.empty?)
+
+              report(num, line, errors, warnings)
+              next
+            end
+
+            yield [num, line, ast_node, nanopub(ast_node, state)]
           end
         else
           enum_for(:each)
         end
       end
 
-      def nanopub(ast_node, state, &block)
+      def nanopub(ast_node, state)
         {
           bel_statement:      serialize(ast_node),
           citation:           citation(state[:citation]),
@@ -43,6 +56,34 @@ module BELParser
         }
       end
 
+      def report(num, line, errors, warnings)
+        warn "Line #{num}: #{line}"
+        errors.each do |err|
+          warn "  #{err}"
+        end
+        warnings.each do |warn|
+          warn "  #{warn}"
+        end
+        warn
+      end
+
+      def errors(ast_node)
+        ast_node
+          .syntax_errors
+          .select do |err|
+            err.is_a?(::BELParser::Language::Syntax::SyntaxError)
+          end.each(&:to_s)
+      end
+
+      def warnings(ast_node)
+        ast_node
+          .syntax_errors
+          .select do |warn|
+            warn.is_a?(::BELParser::Language::Syntax::SyntaxError) ||
+              warn.is_a?(::BELParser::Language::Semantics::SemanticsWarning)
+          end.each(&:to_s)
+      end
+
       def citation(citation)
         citation.each do |field, value|
           citation[field] = unquote(value)
@@ -133,6 +174,6 @@ if __FILE__ == $PROGRAM_NAME
       Validator.new(
         StateAggregator.new(
           FirstNode.new(Filter.new(BELParser::ASTGenerator.new(io))),
-          initial_state))).each.to_a
+          initial_state))).each.map(&:last).to_a
   puts JSON.dump(nanopubs)
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel_parser
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.21
+  version: 1.0.0.alpha.22
 platform: ruby
 authors:
 - Anthony Bargnesi