bel_parser 1.0.0.alpha.7 → 1.0.0.alpha.8
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- checksums.yaml +4 -4
- data/.gemspec +1 -1
- data/VERSION +1 -1
- data/bin/bel2_validator +7 -4
- data/lib/bel_parser/ast_filter.rb +2 -2
- data/lib/bel_parser/ast_generator.rb +11 -18
- data/lib/bel_parser/language/expression_validator.rb +8 -0
- data/lib/bel_parser/language/quoting.rb +19 -22
- data/lib/bel_parser/language/semantics/deeply_nested_statement.rb +65 -0
- data/lib/bel_parser/language/semantics/function_deprecation.rb +36 -0
- data/lib/bel_parser/language/semantics/list_function_subject.rb +45 -0
- data/lib/bel_parser/language/semantics/relationship_deprecation.rb +36 -0
- data/lib/bel_parser/language/semantics/signature_mapping.rb +30 -16
- data/lib/bel_parser/language/semantics.rb +7 -2
- data/lib/bel_parser/language/semantics_ast.rb +22 -12
- data/lib/bel_parser/language/semantics_function.rb +4 -1
- data/lib/bel_parser/language/semantics_result.rb +1 -0
- data/lib/bel_parser/language/semantics_warning.rb +2 -0
- data/lib/bel_parser/language/signature.rb +3 -3
- data/lib/bel_parser/language/syntax/invalid_function.rb +2 -2
- data/lib/bel_parser/language/syntax/invalid_relationship.rb +2 -2
- data/lib/bel_parser/language/syntax/undefined_namespace.rb +0 -1
- data/lib/bel_parser/language/syntax.rb +7 -2
- data/lib/bel_parser/language/syntax_error.rb +2 -0
- data/lib/bel_parser/language/syntax_function.rb +4 -1
- data/lib/bel_parser/language/syntax_result.rb +1 -0
- data/lib/bel_parser/language/syntax_warning.rb +2 -0
- data/lib/bel_parser/language/version1_0/functions/abundance.rb +14 -15
- data/lib/bel_parser/language/version1_0/functions/biological_process.rb +14 -15
- data/lib/bel_parser/language/version1_0/functions/catalytic_activity.rb +25 -21
- data/lib/bel_parser/language/version1_0/functions/cell_secretion.rb +15 -12
- data/lib/bel_parser/language/version1_0/functions/cell_surface_expression.rb +15 -12
- data/lib/bel_parser/language/version1_0/functions/chaperone_activity.rb +25 -21
- data/lib/bel_parser/language/version1_0/functions/complex_abundance.rb +26 -25
- data/lib/bel_parser/language/version1_0/functions/composite_abundance.rb +13 -12
- data/lib/bel_parser/language/version1_0/functions/degradation.rb +15 -12
- data/lib/bel_parser/language/version1_0/functions/fusion.rb +135 -129
- data/lib/bel_parser/language/version1_0/functions/gene_abundance.rb +34 -34
- data/lib/bel_parser/language/version1_0/functions/gtp_bound_activity.rb +24 -21
- data/lib/bel_parser/language/version1_0/functions/kinase_activity.rb +25 -21
- data/lib/bel_parser/language/version1_0/functions/list.rb +24 -24
- data/lib/bel_parser/language/version1_0/functions/micro_rna_abundance.rb +18 -17
- data/lib/bel_parser/language/version1_0/functions/molecular_activity.rb +14 -12
- data/lib/bel_parser/language/version1_0/functions/pathology.rb +14 -15
- data/lib/bel_parser/language/version1_0/functions/peptidase_activity.rb +23 -21
- data/lib/bel_parser/language/version1_0/functions/phosphatase_activity.rb +23 -21
- data/lib/bel_parser/language/version1_0/functions/products.rb +9 -10
- data/lib/bel_parser/language/version1_0/functions/protein_abundance.rb +94 -91
- data/lib/bel_parser/language/version1_0/functions/protein_modification.rb +60 -57
- data/lib/bel_parser/language/version1_0/functions/reactants.rb +9 -10
- data/lib/bel_parser/language/version1_0/functions/reaction.rb +18 -17
- data/lib/bel_parser/language/version1_0/functions/ribosylation_activity.rb +25 -21
- data/lib/bel_parser/language/version1_0/functions/rna_abundance.rb +34 -34
- data/lib/bel_parser/language/version1_0/functions/substitution.rb +29 -28
- data/lib/bel_parser/language/version1_0/functions/transcriptional_activity.rb +25 -21
- data/lib/bel_parser/language/version1_0/functions/translocation.rb +33 -32
- data/lib/bel_parser/language/version1_0/functions/transport_activity.rb +26 -21
- data/lib/bel_parser/language/version1_0/functions/truncation.rb +15 -14
- data/lib/bel_parser/language/version1_0/relationships/acts_in.rb +16 -2
- data/lib/bel_parser/language/version1_0/relationships/analogous.rb +8 -2
- data/lib/bel_parser/language/version1_0/relationships/association.rb +13 -2
- data/lib/bel_parser/language/version1_0/relationships/biomarker_for.rb +9 -2
- data/lib/bel_parser/language/version1_0/relationships/causes_no_change.rb +13 -2
- data/lib/bel_parser/language/version1_0/relationships/decreases.rb +22 -2
- data/lib/bel_parser/language/version1_0/relationships/directly_decreases.rb +11 -2
- data/lib/bel_parser/language/version1_0/relationships/directly_increases.rb +11 -2
- data/lib/bel_parser/language/version1_0/relationships/has_component.rb +25 -2
- data/lib/bel_parser/language/version1_0/relationships/has_components.rb +20 -2
- data/lib/bel_parser/language/version1_0/relationships/has_member.rb +15 -2
- data/lib/bel_parser/language/version1_0/relationships/has_members.rb +20 -2
- data/lib/bel_parser/language/version1_0/relationships/has_modification.rb +13 -2
- data/lib/bel_parser/language/version1_0/relationships/has_product.rb +15 -2
- data/lib/bel_parser/language/version1_0/relationships/has_variant.rb +13 -2
- data/lib/bel_parser/language/version1_0/relationships/includes.rb +18 -2
- data/lib/bel_parser/language/version1_0/relationships/increases.rb +22 -2
- data/lib/bel_parser/language/version1_0/relationships/is_a.rb +15 -2
- data/lib/bel_parser/language/version1_0/relationships/negative_correlation.rb +13 -2
- data/lib/bel_parser/language/version1_0/relationships/orthologous.rb +15 -2
- data/lib/bel_parser/language/version1_0/relationships/positive_correlation.rb +9 -2
- data/lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb +11 -2
- data/lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb +16 -2
- data/lib/bel_parser/language/version1_0/relationships/reactant_in.rb +15 -2
- data/lib/bel_parser/language/version1_0/relationships/sub_process_of.rb +22 -2
- data/lib/bel_parser/language/version1_0/relationships/transcribed_to.rb +12 -2
- data/lib/bel_parser/language/version1_0/relationships/translated_to.rb +13 -2
- data/lib/bel_parser/language/version1_0/relationships/translocates.rb +16 -2
- data/lib/bel_parser/language/version1_0/syntax/function.rb +0 -1
- data/lib/bel_parser/language/version1_0.rb +13 -2
- data/lib/bel_parser/language/version2_0/functions/abundance.rb +54 -53
- data/lib/bel_parser/language/version2_0/functions/activity.rb +8 -5
- data/lib/bel_parser/language/version2_0/functions/biological_process.rb +16 -16
- data/lib/bel_parser/language/version2_0/functions/cell_secretion.rb +15 -12
- data/lib/bel_parser/language/version2_0/functions/cell_surface_expression.rb +15 -12
- data/lib/bel_parser/language/version2_0/functions/complex_abundance.rb +61 -58
- data/lib/bel_parser/language/version2_0/functions/composite_abundance.rb +13 -12
- data/lib/bel_parser/language/version2_0/functions/degradation.rb +15 -12
- data/lib/bel_parser/language/version2_0/functions/fragment.rb +8 -6
- data/lib/bel_parser/language/version2_0/functions/from_location.rb +18 -17
- data/lib/bel_parser/language/version2_0/functions/fusion.rb +120 -117
- data/lib/bel_parser/language/version2_0/functions/gene_abundance.rb +64 -62
- data/lib/bel_parser/language/version2_0/functions/list.rb +24 -24
- data/lib/bel_parser/language/version2_0/functions/location.rb +14 -15
- data/lib/bel_parser/language/version2_0/functions/micro_rna_abundance.rb +58 -55
- data/lib/bel_parser/language/version2_0/functions/molecular_activity.rb +16 -14
- data/lib/bel_parser/language/version2_0/functions/pathology.rb +14 -15
- data/lib/bel_parser/language/version2_0/functions/products.rb +9 -10
- data/lib/bel_parser/language/version2_0/functions/protein_abundance.rb +96 -92
- data/lib/bel_parser/language/version2_0/functions/protein_modification.rb +57 -54
- data/lib/bel_parser/language/version2_0/functions/reactants.rb +9 -10
- data/lib/bel_parser/language/version2_0/functions/reaction.rb +18 -17
- data/lib/bel_parser/language/version2_0/functions/rna_abundance.rb +64 -62
- data/lib/bel_parser/language/version2_0/functions/to_location.rb +16 -16
- data/lib/bel_parser/language/version2_0/functions/translocation.rb +23 -22
- data/lib/bel_parser/language/version2_0/functions/variant.rb +13 -13
- data/lib/bel_parser/language/version2_0/relationships/acts_in.rb +16 -2
- data/lib/bel_parser/language/version2_0/relationships/analogous.rb +8 -2
- data/lib/bel_parser/language/version2_0/relationships/association.rb +13 -2
- data/lib/bel_parser/language/version2_0/relationships/biomarker_for.rb +9 -2
- data/lib/bel_parser/language/version2_0/relationships/causes_no_change.rb +13 -2
- data/lib/bel_parser/language/version2_0/relationships/decreases.rb +22 -2
- data/lib/bel_parser/language/version2_0/relationships/directly_decreases.rb +11 -2
- data/lib/bel_parser/language/version2_0/relationships/directly_increases.rb +11 -2
- data/lib/bel_parser/language/version2_0/relationships/has_component.rb +25 -2
- data/lib/bel_parser/language/version2_0/relationships/has_components.rb +20 -2
- data/lib/bel_parser/language/version2_0/relationships/has_member.rb +15 -2
- data/lib/bel_parser/language/version2_0/relationships/has_members.rb +20 -2
- data/lib/bel_parser/language/version2_0/relationships/has_modification.rb +13 -2
- data/lib/bel_parser/language/version2_0/relationships/has_product.rb +15 -2
- data/lib/bel_parser/language/version2_0/relationships/has_variant.rb +13 -2
- data/lib/bel_parser/language/version2_0/relationships/includes.rb +18 -2
- data/lib/bel_parser/language/version2_0/relationships/increases.rb +22 -2
- data/lib/bel_parser/language/version2_0/relationships/is_a.rb +15 -2
- data/lib/bel_parser/language/version2_0/relationships/negative_correlation.rb +13 -2
- data/lib/bel_parser/language/version2_0/relationships/orthologous.rb +15 -2
- data/lib/bel_parser/language/version2_0/relationships/positive_correlation.rb +9 -2
- data/lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb +11 -2
- data/lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb +16 -2
- data/lib/bel_parser/language/version2_0/relationships/reactant_in.rb +15 -2
- data/lib/bel_parser/language/version2_0/relationships/regulates.rb +14 -2
- data/lib/bel_parser/language/version2_0/relationships/sub_process_of.rb +22 -2
- data/lib/bel_parser/language/version2_0/relationships/transcribed_to.rb +12 -2
- data/lib/bel_parser/language/version2_0/relationships/translated_to.rb +13 -2
- data/lib/bel_parser/language/version2_0/relationships/translocates.rb +16 -2
- data/lib/bel_parser/language.rb +18 -8
- data/lib/bel_parser/parser.rb +1 -0
- data/lib/bel_parser/parsers/ast/node.rb +112 -74
- data/lib/bel_parser/parsers/bel_script/set.rl +1 -1
- data/lib/bel_parser/parsers/bel_script/set_document.rb +7087 -0
- data/lib/bel_parser/parsers/bel_script/set_document.rl +97 -0
- data/lib/bel_parser/parsers/bel_script.rb +1 -0
- data/lib/bel_parser/parsers/common/common.rl +1 -1
- data/lib/bel_parser/script/parser.rb +1 -0
- metadata +8 -2
@@ -7,14 +7,16 @@ module BELParser
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module Language
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module Version2_0
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module Functions
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# ProteinModification: Denotes a covalently modified protein
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# ProteinModification: Denotes a covalently modified protein
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# abundance
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class ProteinModification
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extend Function
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SHORT = :pmod
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LONG = :proteinModification
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RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ProteinModification
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DESCRIPTION = 'Denotes a covalently modified protein
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DESCRIPTION = 'Denotes a covalently modified protein
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bundance'.freeze
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def self.short
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SHORT
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end
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module Signatures
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# ProteinModificationWithTypeSignature
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class ProteinModificationWithTypeSignature
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extend BELParser::Language::Signature
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# TODO: More strict prefix validation for modification type?
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AST = BELParser::Language::Semantics::Builder.build do
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term(
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function(
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identifier(
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function_of(ProteinModification))),
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argument(
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parameter(
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prefix(any),
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value(
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value_type(
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has_encoding,
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encoding_of(:ModificationType))))))
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end
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private_constant :AST
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STRING_FORM
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# ProteinModificationWithTypeAminoSignature
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class ProteinModificationWithTypeAminoSignature
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extend BELParser::Language::Signature
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# TODO: More strict prefix validation for modification type?
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AST = BELParser::Language::Semantics::Builder.build do
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term(
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function(
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identifier(
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function_of(ProteinModification))),
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argument(
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parameter(
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prefix(any),
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value(
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value_type(
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has_encoding,
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encoding_of(:ModificationType))))),
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argument(
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private_constant :AST
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STRING_FORM
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# ProteinModificationWithTypeAminoPositionSignature
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class ProteinModificationWithTypeAminoPositionSignature
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# TODO: More strict prefix validation for modification type?
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AST = BELParser::Language::Semantics::Builder.build do
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term(
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function(
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identifier(
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function_of(ProteinModification))),
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argument(
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parameter(
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prefix(any),
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argument(
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encoding_of(:*))))),
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argument(
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prefix(any),
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encoding_of(:*))))))
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SIGNATURES = Signatures.constants.map do |const|
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end
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module Signatures
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# ReactantsSignature
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class ReactantsSignature
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extend BELParser::Language::Signature
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AST = BELParser::Language::Semantics::Builder.build do
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function(
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identifier(
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function_of(Reactants))),
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variadic_arguments(
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term(
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function(
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identifier(
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return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))))
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private_constant :AST
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STRING_FORM
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end
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end
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SIGNATURES = Signatures.constants.map do |const|
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module Language
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module Version2_0
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module Functions
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# Reaction: Denotes the frequency or abundance of events in
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# Reaction: Denotes the frequency or abundance of events in
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# a reaction
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class Reaction
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extend Function
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SHORT = :rxn
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LONG = :reaction
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RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
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DESCRIPTION = 'Denotes the frequency or abundance of events
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DESCRIPTION = 'Denotes the frequency or abundance of events
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n a reaction'.freeze
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def self.short
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SHORT
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@@ -37,7 +39,7 @@ module BELParser
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end
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module Signatures
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-
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+
# ReactionSignature
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class ReactionSignature
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extend BELParser::Language::Signature
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AST = BELParser::Language::Semantics::Builder.build do
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term(
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function(
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identifier(
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function_of(Reaction))),
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argument(
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term(
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function(
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identifier(
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return_type_of(BELParser::Language::Version2_0::ReturnTypes::Reactants))))),
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argument(
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term(
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function(
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identifier(
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return_type_of(BELParser::Language::Version2_0::ReturnTypes::Products))))))
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end
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private_constant :AST
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STRING_FORM
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end
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end
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-
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end
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SIGNATURES = Signatures.constants.map do |const|
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end
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module Signatures
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-
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+
# RNAAbundanceSignature
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class RNAAbundanceSignature
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extend BELParser::Language::Signature
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AST = BELParser::Language::Semantics::Builder.build do
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term(
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-
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function(
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identifier(
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function_of(RNAAbundance))),
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argument(
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parameter(
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prefix(
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identifier(
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has_namespace,
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namespace_of(:*))),
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value(
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value_type(
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has_encoding,
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encoding_of(:RnaAbundance))))))
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end
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private_constant :AST
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STRING_FORM
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end
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end
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-
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+
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+
# RNAAbundanceWithFusionSignature
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class RNAAbundanceWithFusionSignature
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extend BELParser::Language::Signature
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AST = BELParser::Language::Semantics::Builder.build do
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term(
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-
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function(
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identifier(
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+
function_of(RNAAbundance))),
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+
argument(
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+
term(
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function(
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identifier(
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return_type_of(BELParser::Language::Version2_0::ReturnTypes::Fusion))))))
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end
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private_constant :AST
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@@ -102,7 +103,8 @@ module BELParser
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STRING_FORM
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end
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end
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-
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+
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+
# RNAAbundanceWithLocationSignature
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class RNAAbundanceWithLocationSignature
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extend BELParser::Language::Signature
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@@ -110,24 +112,24 @@ module BELParser
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AST = BELParser::Language::Semantics::Builder.build do
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term(
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-
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-
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function(
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identifier(
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+
function_of(RNAAbundance))),
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argument(
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+
parameter(
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prefix(
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+
identifier(
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+
has_namespace,
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+
namespace_of(:*))),
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+
value(
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+
value_type(
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+
has_encoding,
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+
encoding_of(:RnaAbundance))))),
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argument(
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+
term(
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function(
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identifier(
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+
return_type_of(BELParser::Language::Version2_0::ReturnTypes::Location))))))
|
131
133
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end
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private_constant :AST
|
133
135
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|
@@ -142,7 +144,8 @@ module BELParser
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142
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STRING_FORM
|
143
145
|
end
|
144
146
|
end
|
145
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-
|
147
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+
|
148
|
+
# RNAAbundanceWithVariantSignature
|
146
149
|
class RNAAbundanceWithVariantSignature
|
147
150
|
extend BELParser::Language::Signature
|
148
151
|
|
@@ -150,24 +153,24 @@ module BELParser
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|
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153
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AST = BELParser::Language::Semantics::Builder.build do
|
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term(
|
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-
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-
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-
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170
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-
|
156
|
+
function(
|
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+
identifier(
|
158
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+
function_of(RNAAbundance))),
|
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+
argument(
|
160
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+
parameter(
|
161
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+
prefix(
|
162
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+
identifier(
|
163
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+
has_namespace,
|
164
|
+
namespace_of(:*))),
|
165
|
+
value(
|
166
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+
value_type(
|
167
|
+
has_encoding,
|
168
|
+
encoding_of(:RnaAbundance))))),
|
169
|
+
argument(
|
170
|
+
term(
|
171
|
+
function(
|
172
|
+
identifier(
|
173
|
+
return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
|
171
174
|
end
|
172
175
|
private_constant :AST
|
173
176
|
|
@@ -182,7 +185,6 @@ module BELParser
|
|
182
185
|
STRING_FORM
|
183
186
|
end
|
184
187
|
end
|
185
|
-
|
186
188
|
end
|
187
189
|
|
188
190
|
SIGNATURES = Signatures.constants.map do |const|
|
@@ -14,7 +14,8 @@ module BELParser
|
|
14
14
|
SHORT = :toLoc
|
15
15
|
LONG = :toLocation
|
16
16
|
RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ToLocation
|
17
|
-
DESCRIPTION = 'Denotes the to cellular location of the
|
17
|
+
DESCRIPTION = 'Denotes the to cellular location of the
|
18
|
+
bundance.'.freeze
|
18
19
|
|
19
20
|
def self.short
|
20
21
|
SHORT
|
@@ -37,7 +38,7 @@ module BELParser
|
|
37
38
|
end
|
38
39
|
|
39
40
|
module Signatures
|
40
|
-
|
41
|
+
# ToLocationSignature
|
41
42
|
class ToLocationSignature
|
42
43
|
extend BELParser::Language::Signature
|
43
44
|
|
@@ -45,19 +46,19 @@ module BELParser
|
|
45
46
|
|
46
47
|
AST = BELParser::Language::Semantics::Builder.build do
|
47
48
|
term(
|
48
|
-
|
49
|
-
|
50
|
-
|
51
|
-
|
52
|
-
|
53
|
-
|
54
|
-
|
55
|
-
|
56
|
-
|
57
|
-
|
58
|
-
|
59
|
-
|
60
|
-
|
49
|
+
function(
|
50
|
+
identifier(
|
51
|
+
function_of(ToLocation))),
|
52
|
+
argument(
|
53
|
+
parameter(
|
54
|
+
prefix(
|
55
|
+
identifier(
|
56
|
+
has_namespace,
|
57
|
+
namespace_of(:*))),
|
58
|
+
value(
|
59
|
+
value_type(
|
60
|
+
has_encoding,
|
61
|
+
encoding_of(:Location))))))
|
61
62
|
end
|
62
63
|
private_constant :AST
|
63
64
|
|
@@ -72,7 +73,6 @@ module BELParser
|
|
72
73
|
STRING_FORM
|
73
74
|
end
|
74
75
|
end
|
75
|
-
|
76
76
|
end
|
77
77
|
|
78
78
|
SIGNATURES = Signatures.constants.map do |const|
|
@@ -7,14 +7,16 @@ module BELParser
|
|
7
7
|
module Language
|
8
8
|
module Version2_0
|
9
9
|
module Functions
|
10
|
-
# Translocation: Denotes the frequency or abundance of events
|
10
|
+
# Translocation: Denotes the frequency or abundance of events
|
11
|
+
# in which members move between locations
|
11
12
|
class Translocation
|
12
13
|
extend Function
|
13
14
|
|
14
15
|
SHORT = :tloc
|
15
16
|
LONG = :translocation
|
16
17
|
RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
|
17
|
-
DESCRIPTION = 'Denotes the frequency or abundance of events
|
18
|
+
DESCRIPTION = 'Denotes the frequency or abundance of events
|
19
|
+
n which members move between locations'.freeze
|
18
20
|
|
19
21
|
def self.short
|
20
22
|
SHORT
|
@@ -37,7 +39,7 @@ module BELParser
|
|
37
39
|
end
|
38
40
|
|
39
41
|
module Signatures
|
40
|
-
|
42
|
+
# TranslocationSignature
|
41
43
|
class TranslocationSignature
|
42
44
|
extend BELParser::Language::Signature
|
43
45
|
|
@@ -45,24 +47,24 @@ module BELParser
|
|
45
47
|
|
46
48
|
AST = BELParser::Language::Semantics::Builder.build do
|
47
49
|
term(
|
48
|
-
|
49
|
-
|
50
|
-
|
51
|
-
|
52
|
-
|
53
|
-
|
54
|
-
|
55
|
-
|
56
|
-
|
57
|
-
|
58
|
-
|
59
|
-
|
60
|
-
|
61
|
-
|
62
|
-
|
63
|
-
|
64
|
-
|
65
|
-
|
50
|
+
function(
|
51
|
+
identifier(
|
52
|
+
function_of(Translocation))),
|
53
|
+
argument(
|
54
|
+
term(
|
55
|
+
function(
|
56
|
+
identifier(
|
57
|
+
return_type_of(BELParser::Language::Version2_0::ReturnTypes::Abundance))))),
|
58
|
+
argument(
|
59
|
+
term(
|
60
|
+
function(
|
61
|
+
identifier(
|
62
|
+
return_type_of(BELParser::Language::Version2_0::ReturnTypes::FromLocation))))),
|
63
|
+
argument(
|
64
|
+
term(
|
65
|
+
function(
|
66
|
+
identifier(
|
67
|
+
return_type_of(BELParser::Language::Version2_0::ReturnTypes::ToLocation))))))
|
66
68
|
end
|
67
69
|
private_constant :AST
|
68
70
|
|
@@ -77,7 +79,6 @@ module BELParser
|
|
77
79
|
STRING_FORM
|
78
80
|
end
|
79
81
|
end
|
80
|
-
|
81
82
|
end
|
82
83
|
|
83
84
|
SIGNATURES = Signatures.constants.map do |const|
|
@@ -14,7 +14,8 @@ module BELParser
|
|
14
14
|
SHORT = :var
|
15
15
|
LONG = :variant
|
16
16
|
RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Variant
|
17
|
-
DESCRIPTION = 'Denotes a sequence variant of the specified
|
17
|
+
DESCRIPTION = 'Denotes a sequence variant of the specified
|
18
|
+
bundance.'.freeze
|
18
19
|
|
19
20
|
def self.short
|
20
21
|
SHORT
|
@@ -37,7 +38,7 @@ module BELParser
|
|
37
38
|
end
|
38
39
|
|
39
40
|
module Signatures
|
40
|
-
|
41
|
+
# VariantSignature
|
41
42
|
class VariantSignature
|
42
43
|
extend BELParser::Language::Signature
|
43
44
|
|
@@ -46,16 +47,16 @@ module BELParser
|
|
46
47
|
# TODO: More strict prefix validation for variant namespace?
|
47
48
|
AST = BELParser::Language::Semantics::Builder.build do
|
48
49
|
term(
|
49
|
-
|
50
|
-
|
51
|
-
|
52
|
-
|
53
|
-
|
54
|
-
|
55
|
-
|
56
|
-
|
57
|
-
|
58
|
-
|
50
|
+
function(
|
51
|
+
identifier(
|
52
|
+
function_of(Variant))),
|
53
|
+
argument(
|
54
|
+
parameter(
|
55
|
+
prefix(any),
|
56
|
+
value(
|
57
|
+
value_type(
|
58
|
+
has_encoding,
|
59
|
+
encoding_of(:HgvsVariantDescription))))))
|
59
60
|
end
|
60
61
|
private_constant :AST
|
61
62
|
|
@@ -70,7 +71,6 @@ module BELParser
|
|
70
71
|
STRING_FORM
|
71
72
|
end
|
72
73
|
end
|
73
|
-
|
74
74
|
end
|
75
75
|
|
76
76
|
SIGNATURES = Signatures.constants.map do |const|
|