bel_parser 1.0.0.alpha.47-java → 1.0.0.alpha.48-java
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- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/lib/bel_parser/expression/model/namespace.rb +60 -20
- data/lib/bel_parser/expression/model/parameter.rb +30 -36
- data/lib/bel_parser/expression/model/statement.rb +28 -3
- data/lib/bel_parser/expression/model/term.rb +46 -7
- data/lib/bel_parser/expression/parser.rb +15 -3
- data/lib/bel_parser/expression/validator.rb +13 -15
- data/lib/bel_parser/language/apply_namespace_encoding.rb +14 -18
- data/lib/bel_parser/language/expression_validator.rb +398 -23
- data/lib/bel_parser/language/semantics_ast_warnings.rb +1 -1
- data/lib/bel_parser/language/specification.rb +4 -0
- data/lib/bel_parser/language/syntax/undefined_namespace.rb +1 -1
- data/lib/bel_parser/language/syntax/undefined_namespace_value.rb +2 -1
- data/lib/bel_parser/language/version2_0/functions/activity.rb +2 -2
- data/lib/bel_parser/language/version2_0/functions/biological_process.rb +1 -2
- data/lib/bel_parser/language/version2_0/functions/cell_secretion.rb +2 -2
- data/lib/bel_parser/language/version2_0/functions/cell_surface_expression.rb +2 -2
- data/lib/bel_parser/language/version2_0/functions/complex_abundance.rb +1 -1
- data/lib/bel_parser/language/version2_0/functions/composite_abundance.rb +1 -1
- data/lib/bel_parser/language/version2_0/functions/degradation.rb +2 -2
- data/lib/bel_parser/language/version2_0/functions/fragment.rb +1 -1
- data/lib/bel_parser/language/version2_0/functions/from_location.rb +1 -1
- data/lib/bel_parser/language/version2_0/functions/fusion.rb +1 -1
- data/lib/bel_parser/language/version2_0/functions/micro_rna_abundance.rb +1 -1
- data/lib/bel_parser/language/version2_0/functions/molecular_activity.rb +1 -1
- data/lib/bel_parser/language/version2_0/functions/protein_modification.rb +1 -1
- data/lib/bel_parser/language/version2_0/functions/reaction.rb +1 -1
- data/lib/bel_parser/language/version2_0/functions/to_location.rb +1 -1
- data/lib/bel_parser/language/version2_0/functions/translocation.rb +1 -1
- data/lib/bel_parser/language/version2_0/functions/variant.rb +1 -1
- data/lib/bel_parser/resource.rb +8 -6
- data/lib/bel_parser/resource/concept_scheme.rb +8 -0
- data/lib/bel_parser/resource/dataset.rb +24 -0
- data/lib/bel_parser/resource/file_resource.rb +8 -0
- data/lib/bel_parser/resource/file_resource_value.rb +1 -0
- data/lib/bel_parser/resource/sparql_reader.rb +3 -1
- data/lib/bel_parser/resource/value.rb +20 -0
- metadata +1 -1
@@ -24,10 +24,38 @@ module BELParser
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# @return [BELParser::Language::Syntax::SyntaxResult] syntax results
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def validate(expression_node)
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@transform.process(expression_node)
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-
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+
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case expression_node
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when BELParser::Parsers::AST::SimpleStatement
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SimpleStatementResult.new(
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validate(expression_node.statement.subject.term),
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validate(expression_node.statement.object.child),
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syntax(expression_node),
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semantics(expression_node))
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when BELParser::Parsers::AST::ObservedTerm
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ObservedTermResult.new(
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validate(expression_node.statement.subject.term),
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syntax(expression_node),
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semantics(expression_node))
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when BELParser::Parsers::AST::NestedStatement
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NestedStatementResult.new(
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validate(expression_node.statement.subject.term),
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validate(expression_node.statement.object.child),
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syntax(expression_node),
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semantics(expression_node))
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when BELParser::Parsers::AST::Statement
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SimpleStatementResult.new(
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validate(expression_node.subject.term),
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validate(expression_node.object.child),
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syntax(expression_node),
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semantics(expression_node))
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when BELParser::Parsers::AST::Term
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TermResult.new(syntax(expression_node), semantics(expression_node))
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when BELParser::Parsers::AST::Parameter
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ParameterResult.new(syntax(expression_node), semantics(expression_node))
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else
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nil
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end
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end
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private
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@@ -39,29 +67,376 @@ module BELParser
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end
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def semantics(expression_node)
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expression_node.traverse.flat_map do |node|
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@semantics_functions.flat_map { |func| func.map(node, @spec, @namespaces) }
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end.compact
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end
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module Result
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def valid?
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valid_syntax? && valid_semantics?
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end
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def valid_syntax?
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@syntax_results.empty?
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end
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def valid_semantics?
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@semantics_results.empty?
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end
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def valid_signature_mappings
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@semantics_results
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.select do |res|
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res.is_a?(Semantics::SignatureMappingSuccess)
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end.uniq
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end
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def invalid_signature_mappings
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@semantics_results
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.select do |res|
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res.is_a?(Semantics::SignatureMappingWarning)
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end
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end
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def detail
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''
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end
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def to_s
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<<-HEADER.gsub(/^ {12}/, '')
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Syntax: #{valid_syntax? ? 'Valid' : 'Invalid'}
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Semantics: #{valid_semantics? ? 'Valid' : 'Invalid'}
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#{syntax_errors_s}#{semantics_errors_s}#{detail}
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HEADER
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end
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private
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def syntax_errors_s
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return nil if @syntax_results.empty?
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report = "Syntax errors\n"
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@syntax_results.each { |res| report += "#{res}\n" }
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report
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end
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def semantics_errors_s
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return nil if @semantics_results.empty?
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report = "Semantic errors\n"
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@semantics_results.each { |res| report += "#{res}\n" }
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report
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end
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end
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class ParameterResult
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attr_reader :syntax_results, :semantics_results
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include Result
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def initialize(syntax_results, semantics_results)
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@syntax_results = syntax_results
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@semantics_results = semantics_results
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end
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def valid_signature_mappings
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nil
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end
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def invalid_signature_mappings
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nil
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end
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end
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class TermResult
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attr_reader :syntax_results, :semantics_results
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include Result
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def initialize(syntax_results, semantics_results)
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@syntax_results = syntax_results
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@semantics_results = semantics_results
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end
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def valid_semantics?
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@semantics_results.any? do |res|
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res.is_a?(Semantics::SignatureMappingSuccess)
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end
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end
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def detail
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report = "Valid signatures\n"
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valid_signature_mappings.each do |mapping|
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report += " #{mapping.signature}\n"
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mapping.results.each do |reason|
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report += " #{reason}\n"
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end
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end
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report += "\n"
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report += "Invalid signatures\n"
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invalid_signature_mappings.each do |mapping|
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report += " #{mapping.signature}\n"
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mapping.results.each do |reason|
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report += " #{reason}\n"
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end
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end
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report
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end
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end
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class ObservedTermResult
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attr_reader :syntax_results, :semantics_results
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include Result
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def initialize(subject_result, syntax, semantics)
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@subject_result = subject_result
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@syntax_results = syntax
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@semantics_results =
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semantics.reject! do |res|
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res.is_a?(Semantics::SignatureMappingWarning) ||
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res.is_a?(Semantics::SignatureMappingSuccess)
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end
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end
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def valid_syntax?
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@subject_result.valid_syntax? && @syntax_results.empty?
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end
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def valid_semantics?
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@subject_result.valid_semantics? && @semantics_results.empty?
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end
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def subject_valid?
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valid?
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end
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def detail
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report = "Subject term - Valid signatures\n"
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@subject_result.valid_signature_mappings.each do |mapping|
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report += " #{mapping.signature}\n"
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mapping.results.each do |reason|
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report += " #{reason}\n"
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end
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end
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report += "\n"
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report += "Subject term - Invalid signatures\n"
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@subject_result.invalid_signature_mappings.each do |mapping|
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report += " #{mapping.signature}\n"
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mapping.results.each do |reason|
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report += " #{reason}\n"
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end
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end
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report
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end
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end
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class SimpleStatementResult
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attr_reader :syntax_results, :semantics_results
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include Result
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def initialize(subject_result, object_result, syntax, semantics)
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@subject_result = subject_result
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@object_result = object_result
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@syntax_results = syntax
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@semantics_results =
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semantics.reject! do |res|
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res.is_a?(Semantics::SignatureMappingWarning) ||
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res.is_a?(Semantics::SignatureMappingSuccess)
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end
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end
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def valid?
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valid_syntax? && valid_semantics?
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end
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def valid_syntax?
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@subject_result.valid_syntax? &&
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@object_result.valid_syntax? &&
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@syntax_results.empty?
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end
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def valid_semantics?
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@subject_result.valid_semantics? &&
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@object_result.valid_semantics? &&
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@semantics_results.empty?
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end
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def subject_valid?
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@subject_result.valid?
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end
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def object_valid?
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@object_result.valid?
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end
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def valid_subject_signatures
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@subject_result.semantics_results
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.select do |res|
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res.is_a?(Semantics::SignatureMappingSuccess)
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end.uniq
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end
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def invalid_subject_signatures
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@subject_result.semantics_results
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.select do |res|
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res.is_a?(Semantics::SignatureMappingWarning)
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end
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end
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def valid_object_signatures
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@object_result.semantics_results
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.select do |res|
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res.is_a?(Semantics::SignatureMappingSuccess)
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end.uniq
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end
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def invalid_object_signatures
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@object_result.semantics_results
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.select do |res|
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res.is_a?(Semantics::SignatureMappingWarning)
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end
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end
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def detail
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report = "Subject term - Valid signatures\n"
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@subject_result.valid_signature_mappings.each do |mapping|
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report += " #{mapping.signature}\n"
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mapping.results.each do |reason|
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report += " #{reason}\n"
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end
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end
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report += "\n"
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report += "Subject term - Invalid signatures\n"
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@subject_result.invalid_signature_mappings.each do |mapping|
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report += " #{mapping.signature}\n"
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mapping.results.each do |reason|
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report += " #{reason}\n"
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end
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end
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report += "\n"
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report += "Object term - Valid signatures\n"
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@object_result.valid_signature_mappings.each do |mapping|
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report += " #{mapping.signature}\n"
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mapping.results.each do |reason|
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report += " #{reason}\n"
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end
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end
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report += "\n"
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report += "Object term - Invalid signatures\n"
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@object_result.invalid_signature_mappings.each do |mapping|
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report += " #{mapping.signature}\n"
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mapping.results.each do |reason|
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report += " #{reason}\n"
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end
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end
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-
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report
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end
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end
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class NestedStatementResult
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attr_reader :syntax_results, :semantics_results
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include Result
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def initialize(subject_result, object_result, syntax, semantics)
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@subject_result = subject_result
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@object_result = object_result
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@syntax_results = syntax
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@semantics_results =
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semantics.reject! do |res|
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res.is_a?(Semantics::SignatureMappingWarning) ||
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res.is_a?(Semantics::SignatureMappingSuccess)
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end
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end
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def valid?
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valid_syntax? && valid_semantics?
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end
|
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def valid_syntax?
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@subject_result.valid_syntax? &&
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@object_result.valid_syntax? &&
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@syntax_results.empty?
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end
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def valid_semantics?
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@subject_result.valid_semantics? &&
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@object_result.valid_semantics? &&
|
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@semantics_results.empty?
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end
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def subject_valid?
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@subject_result.valid?
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+
end
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+
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376
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def object_valid?
|
377
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@object_result.valid?
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378
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+
end
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379
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+
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380
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def valid_subject_signatures
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381
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@subject_result.semantics_results
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382
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.select do |res|
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383
|
+
res.is_a?(Semantics::SignatureMappingSuccess)
|
384
|
+
end.uniq
|
385
|
+
end
|
386
|
+
|
387
|
+
def invalid_subject_signatures
|
388
|
+
@subject_result.semantics_results
|
389
|
+
.select do |res|
|
390
|
+
res.is_a?(Semantics::SignatureMappingWarning)
|
391
|
+
end
|
392
|
+
end
|
393
|
+
|
394
|
+
def valid_object_signatures
|
395
|
+
@object_result.semantics_results
|
396
|
+
.select do |res|
|
397
|
+
res.is_a?(Semantics::SignatureMappingSuccess)
|
398
|
+
end.uniq
|
399
|
+
end
|
400
|
+
|
401
|
+
def invalid_object_signatures
|
402
|
+
@object_result.semantics_results
|
403
|
+
.select do |res|
|
404
|
+
res.is_a?(Semantics::SignatureMappingWarning)
|
405
|
+
end
|
406
|
+
end
|
407
|
+
|
408
|
+
def to_s
|
409
|
+
report = @object_result.to_s
|
410
|
+
<<-HEADER.gsub(/^ {12}/, '')
|
411
|
+
Syntax: #{valid_syntax? ? 'Valid' : 'Invalid'}
|
412
|
+
Semantics: #{valid_semantics? ? 'Valid' : 'Invalid'}
|
413
|
+
|
414
|
+
#{syntax_errors_s}#{semantics_errors_s}#{detail}
|
415
|
+
HEADER
|
416
|
+
end
|
417
|
+
|
418
|
+
def detail
|
419
|
+
report = "Subject term - Valid signatures\n"
|
420
|
+
@subject_result.valid_signature_mappings.each do |mapping|
|
421
|
+
report += " #{mapping.signature}\n"
|
422
|
+
mapping.results.each do |reason|
|
423
|
+
report += " #{reason}\n"
|
424
|
+
end
|
425
|
+
end
|
426
|
+
report += "\n"
|
427
|
+
|
428
|
+
report += "Subject term - Invalid signatures\n"
|
429
|
+
@subject_result.invalid_signature_mappings.each do |mapping|
|
430
|
+
report += " #{mapping.signature}\n"
|
431
|
+
mapping.results.each do |reason|
|
432
|
+
report += " #{reason}\n"
|
433
|
+
end
|
434
|
+
end
|
435
|
+
report += "\n"
|
436
|
+
|
437
|
+
report += @object_result.detail
|
438
|
+
report
|
439
|
+
end
|
65
440
|
end
|
66
441
|
end
|
67
442
|
end
|
@@ -126,7 +126,7 @@ module BELParser
|
|
126
126
|
|
127
127
|
def to_s
|
128
128
|
function = @expression_node.string_literal
|
129
|
-
%(Function of "#{function}" does not match return types: #{@expected_return_types.join(', ')})
|
129
|
+
%(Function of "#{function}" does not match return types: #{@expected_return_types.map(&:to_sym).join(', ')})
|
130
130
|
end
|
131
131
|
end
|
132
132
|
|