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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# MicroRNAAbundance: Denotes the abundance of a processed,
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# MicroRNAAbundance: Denotes the abundance of a processed,
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# functional microRNA
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class MicroRNAAbundance
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extend Function
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SHORT = :m
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LONG = :microRNAAbundance
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RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::MicroRNAAbundance
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DESCRIPTION = 'Denotes the abundance of a processed, functional
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DESCRIPTION = 'Denotes the abundance of a processed, functional
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icroRNA'.freeze
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def self.short
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SHORT
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module Signatures
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# MicroRNAAbundanceSignature
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class MicroRNAAbundanceSignature
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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(MicroRNAAbundance))),
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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(:MicroRNAAbundance))))))
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STRING_FORM
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# MicroRNAAbundanceWithLocationSignature
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class MicroRNAAbundanceWithLocationSignature
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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(MicroRNAAbundance))),
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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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encoding_of(:MicroRNAAbundance))))),
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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))))))
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# MicroRNAAbundanceWithVariantSignature
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class MicroRNAAbundanceWithVariantSignature
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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(MicroRNAAbundance))),
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argument(
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parameter(
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prefix(
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namespace_of(:*))),
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value(
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value_type(
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encoding_of(:MicroRNAAbundance))))),
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argument(
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term(
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function(
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private_constant :AST
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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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# MolecularActivity: Denotes the frequency or abundance of events
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# MolecularActivity: Denotes the frequency or abundance of events
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# in which a member acts as a causal agent at the molecular scale
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class MolecularActivity
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extend Function
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SHORT = :ma
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LONG = :molecularActivity
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RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::MolecularActivity
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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 which a member acts as a causal agent at the
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olecular scale'.freeze
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def self.short
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module Signatures
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# MolecularActivitySignature
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class MolecularActivitySignature
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extend BELParser::Language::Signature
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# TODO: More constraints on prefix for activity namespace?
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AST = BELParser::Language::Semantics::Builder.build do
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function(
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argument(
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prefix(any),
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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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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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# PathologySignature
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class PathologySignature
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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(Pathology))),
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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(:Pathology))))))
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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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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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# ProductsSignature
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class ProductsSignature
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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(Products))),
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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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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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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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+
# ProteinAbundanceSignature
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class ProteinAbundanceSignature
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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(ProteinAbundance))),
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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(:ProteinAbundance))))))
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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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# ProteinAbundanceWithFragmentSignature
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class ProteinAbundanceWithFragmentSignature
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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(ProteinAbundance))),
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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(:ProteinAbundance))))),
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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::Fragment))))))
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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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+
# ProteinAbundanceWithFusionSignature
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class ProteinAbundanceWithFusionSignature
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extend BELParser::Language::Signature
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@@ -142,7 +144,8 @@ 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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+
# ProteinAbundanceWithLocationSignature
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class ProteinAbundanceWithLocationSignature
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extend BELParser::Language::Signature
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@@ -150,24 +153,24 @@ module BELParser
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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(ProteinAbundance))),
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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(:ProteinAbundance))))),
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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))))))
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end
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private_constant :AST
|
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@@ -182,7 +185,8 @@ module BELParser
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182
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|
STRING_FORM
|
183
186
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end
|
184
187
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end
|
185
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-
|
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|
+
|
189
|
+
# ProteinAbundanceWithProteinModificationSignature
|
186
190
|
class ProteinAbundanceWithProteinModificationSignature
|
187
191
|
extend BELParser::Language::Signature
|
188
192
|
|
@@ -190,24 +194,24 @@ module BELParser
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|
190
194
|
|
191
195
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AST = BELParser::Language::Semantics::Builder.build do
|
192
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term(
|
193
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-
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-
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|
+
function(
|
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+
identifier(
|
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+
function_of(ProteinAbundance))),
|
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+
argument(
|
201
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+
parameter(
|
202
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+
prefix(
|
203
|
+
identifier(
|
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|
+
has_namespace,
|
205
|
+
namespace_of(:*))),
|
206
|
+
value(
|
207
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+
value_type(
|
208
|
+
has_encoding,
|
209
|
+
encoding_of(:ProteinAbundance))))),
|
210
|
+
variadic_arguments(
|
211
|
+
term(
|
212
|
+
function(
|
213
|
+
identifier(
|
214
|
+
return_type_of(BELParser::Language::Version2_0::ReturnTypes::ProteinModification))))))
|
211
215
|
end
|
212
216
|
private_constant :AST
|
213
217
|
|
@@ -222,7 +226,8 @@ module BELParser
|
|
222
226
|
STRING_FORM
|
223
227
|
end
|
224
228
|
end
|
225
|
-
|
229
|
+
|
230
|
+
# ProteinAbundanceWithVariantSignature
|
226
231
|
class ProteinAbundanceWithVariantSignature
|
227
232
|
extend BELParser::Language::Signature
|
228
233
|
|
@@ -230,24 +235,24 @@ module BELParser
|
|
230
235
|
|
231
236
|
AST = BELParser::Language::Semantics::Builder.build do
|
232
237
|
term(
|
233
|
-
|
234
|
-
|
235
|
-
|
236
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-
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-
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|
-
|
250
|
-
|
238
|
+
function(
|
239
|
+
identifier(
|
240
|
+
function_of(ProteinAbundance))),
|
241
|
+
argument(
|
242
|
+
parameter(
|
243
|
+
prefix(
|
244
|
+
identifier(
|
245
|
+
has_namespace,
|
246
|
+
namespace_of(:*))),
|
247
|
+
value(
|
248
|
+
value_type(
|
249
|
+
has_encoding,
|
250
|
+
encoding_of(:ProteinAbundance))))),
|
251
|
+
argument(
|
252
|
+
term(
|
253
|
+
function(
|
254
|
+
identifier(
|
255
|
+
return_type_of(BELParser::Language::Version2_0::ReturnTypes::Variant))))))
|
251
256
|
end
|
252
257
|
private_constant :AST
|
253
258
|
|
@@ -262,7 +267,6 @@ module BELParser
|
|
262
267
|
STRING_FORM
|
263
268
|
end
|
264
269
|
end
|
265
|
-
|
266
270
|
end
|
267
271
|
|
268
272
|
SIGNATURES = Signatures.constants.map do |const|
|