bel_parser 1.0.0.alpha.1 → 1.0.0.alpha.2
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- checksums.yaml +4 -4
- data/.gemspec +1 -1
- data/VERSION +1 -1
- data/bin/bel2_termcheck +2 -2
- data/lib/bel_parser/expression/term_semantics.rb +2 -2
- data/lib/bel_parser/language/expression_validator.rb +42 -0
- data/lib/bel_parser/language/function.rb +8 -0
- data/lib/bel_parser/language/relationship.rb +57 -0
- data/lib/bel_parser/language/{semantic_ast.rb → semantics/semantic_ast.rb} +5 -27
- data/lib/bel_parser/language/semantics/semantic_match.rb +28 -0
- data/lib/bel_parser/language/semantics.rb +2 -0
- data/lib/bel_parser/language/specification.rb +34 -10
- data/lib/bel_parser/language/syntax.rb +0 -0
- data/lib/bel_parser/language/{version1 → version1_0}/functions/abundance.rb +4 -4
- data/lib/bel_parser/language/{version1 → version1_0}/functions/biological_process.rb +4 -4
- data/lib/bel_parser/language/{version1 → version1_0}/functions/catalytic_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/cell_secretion.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/cell_surface_expression.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/chaperone_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/complex_abundance.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/composite_abundance.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/degradation.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/fusion.rb +4 -4
- data/lib/bel_parser/language/{version1 → version1_0}/functions/gene_abundance.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/gtp_bound_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/kinase_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/list.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/micro_rna_abundance.rb +4 -4
- data/lib/bel_parser/language/{version1 → version1_0}/functions/molecular_activity.rb +5 -5
- data/lib/bel_parser/language/{version2 → version1_0}/functions/pathology.rb +4 -4
- data/lib/bel_parser/language/{version1 → version1_0}/functions/peptidase_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/phosphatase_activity.rb +6 -6
- data/lib/bel_parser/language/{version2 → version1_0}/functions/products.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/protein_abundance.rb +8 -8
- data/lib/bel_parser/language/{version1 → version1_0}/functions/protein_modification.rb +4 -4
- data/lib/bel_parser/language/{version2 → version1_0}/functions/reactants.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/reaction.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/ribosylation_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/rna_abundance.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/substitution.rb +4 -4
- data/lib/bel_parser/language/{version1 → version1_0}/functions/transcriptional_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/translocation.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/transport_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/truncation.rb +4 -4
- data/lib/bel_parser/language/version1_0/relationships/acts_in.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/analogous.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/association.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/biomarker_for.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/causes_no_change.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/decreases.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/directly_decreases.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/directly_increases.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/has_component.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/has_components.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/has_member.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/has_members.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/has_modification.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/has_product.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/has_variant.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/includes.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/increases.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/is_a.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/negative_correlation.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/orthologous.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/positive_correlation.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/reactant_in.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/sub_process_of.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/transcribed_to.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/translated_to.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/translocates.rb +31 -0
- data/lib/bel_parser/language/{version2 → version1_0}/return_types/abundance.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/any.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/biological_process.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/catalytic_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/chaperone_activity.rb +1 -1
- data/lib/bel_parser/language/{version2 → version1_0}/return_types/complex_abundance.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/fusion.rb +1 -1
- data/lib/bel_parser/language/{version2 → version1_0}/return_types/gene_abundance.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/gtp_bound_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/kinase_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/list.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/micro_rna_abundance.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/molecular_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/pathology.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/peptidase_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/phosphatase_activity.rb +1 -1
- data/lib/bel_parser/language/{version2 → version1_0}/return_types/products.rb +1 -1
- data/lib/bel_parser/language/{version2 → version1_0}/return_types/protein_abundance.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/protein_modification.rb +1 -1
- data/lib/bel_parser/language/{version2 → version1_0}/return_types/reactants.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/ribosylation_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/rna_abundance.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/substitution.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/transcriptional_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/transport_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/truncation.rb +1 -1
- data/lib/bel_parser/language/version1_0/syntax/function.rb +29 -0
- data/lib/bel_parser/language/version1_0.rb +89 -0
- data/lib/bel_parser/language/{version2 → version2_0}/functions/abundance.rb +6 -6
- data/lib/bel_parser/language/{version2 → version2_0}/functions/activity.rb +7 -7
- data/lib/bel_parser/language/{version2 → version2_0}/functions/biological_process.rb +4 -4
- data/lib/bel_parser/language/{version2 → version2_0}/functions/cell_secretion.rb +5 -5
- data/lib/bel_parser/language/{version2 → version2_0}/functions/cell_surface_expression.rb +5 -5
- data/lib/bel_parser/language/{version2 → version2_0}/functions/complex_abundance.rb +8 -8
- data/lib/bel_parser/language/{version2 → version2_0}/functions/composite_abundance.rb +5 -5
- data/lib/bel_parser/language/{version2 → version2_0}/functions/degradation.rb +5 -5
- data/lib/bel_parser/language/{version2 → version2_0}/functions/fragment.rb +4 -4
- data/lib/bel_parser/language/{version2 → version2_0}/functions/from_location.rb +4 -4
- data/lib/bel_parser/language/{version2 → version2_0}/functions/fusion.rb +4 -4
- data/lib/bel_parser/language/{version2 → version2_0}/functions/gene_abundance.rb +7 -7
- data/lib/bel_parser/language/{version2 → version2_0}/functions/list.rb +5 -5
- data/lib/bel_parser/language/{version2 → version2_0}/functions/location.rb +4 -4
- data/lib/bel_parser/language/{version2 → version2_0}/functions/micro_rna_abundance.rb +6 -6
- data/lib/bel_parser/language/{version2 → version2_0}/functions/molecular_activity.rb +4 -4
- data/lib/bel_parser/language/{version1 → version2_0}/functions/pathology.rb +4 -4
- data/lib/bel_parser/language/{version1 → version2_0}/functions/products.rb +5 -5
- data/lib/bel_parser/language/{version2 → version2_0}/functions/protein_abundance.rb +9 -9
- data/lib/bel_parser/language/{version2 → version2_0}/functions/protein_modification.rb +7 -7
- data/lib/bel_parser/language/{version1 → version2_0}/functions/reactants.rb +5 -5
- data/lib/bel_parser/language/{version2 → version2_0}/functions/reaction.rb +6 -6
- data/lib/bel_parser/language/{version2 → version2_0}/functions/rna_abundance.rb +11 -11
- data/lib/bel_parser/language/{version2 → version2_0}/functions/to_location.rb +4 -4
- data/lib/bel_parser/language/{version2 → version2_0}/functions/translocation.rb +8 -8
- data/lib/bel_parser/language/{version2 → version2_0}/functions/variant.rb +4 -4
- data/lib/bel_parser/language/version2_0/relationships/acts_in.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/analogous.rb +35 -0
- data/lib/bel_parser/language/version2_0/relationships/association.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/biomarker_for.rb +35 -0
- data/lib/bel_parser/language/version2_0/relationships/causes_no_change.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/decreases.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/directly_decreases.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/directly_increases.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/has_component.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/has_components.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/has_member.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/has_members.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/has_modification.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/has_product.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/has_variant.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/includes.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/increases.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/is_a.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/negative_correlation.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/orthologous.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/positive_correlation.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb +35 -0
- data/lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/reactant_in.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/regulates.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/sub_process_of.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/transcribed_to.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/translated_to.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/translocates.rb +31 -0
- data/lib/bel_parser/language/{version1 → version2_0}/return_types/abundance.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/activity.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/any.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/biological_process.rb +1 -1
- data/lib/bel_parser/language/{version1 → version2_0}/return_types/complex_abundance.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/fragment.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/from_location.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/fusion.rb +1 -1
- data/lib/bel_parser/language/{version1 → version2_0}/return_types/gene_abundance.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/list.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/location.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/micro_rna_abundance.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/molecular_activity.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/pathology.rb +1 -1
- data/lib/bel_parser/language/{version1 → version2_0}/return_types/products.rb +1 -1
- data/lib/bel_parser/language/{version1 → version2_0}/return_types/protein_abundance.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/protein_modification.rb +1 -1
- data/lib/bel_parser/language/{version1 → version2_0}/return_types/reactants.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/rna_abundance.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/to_location.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/variant.rb +1 -1
- data/lib/bel_parser/language/version2_0.rb +73 -0
- data/lib/bel_parser/language.rb +90 -2
- data/lib/bel_parser/parsers/ast/node.rb +11 -1
- metadata +172 -111
- data/lib/bel_parser/language/syntax/expression/incomplete_node.rb +0 -14
- data/lib/bel_parser/language/syntax/expression/invalid_term_function.rb +0 -22
- data/lib/bel_parser/language/version1.rb +0 -50
- data/lib/bel_parser/language/version2.rb +0 -50
metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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name: bel_parser
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version: !ruby/object:Gem::Version
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version: 1.0.0.alpha.
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version: 1.0.0.alpha.2
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platform: ruby
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authors:
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- Anthony Bargnesi
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2016-04-
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+
date: 2016-04-08 00:00:00.000000000 Z
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dependencies: []
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description: Implements language versions 1.0 and 2.0.
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email: abargnesi@selventa.com
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@@ -31,120 +31,181 @@ files:
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- lib/bel_parser/expression/parser.rb
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- lib/bel_parser/expression/term_semantics.rb
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- lib/bel_parser/language.rb
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- lib/bel_parser/language/expression_validator.rb
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- lib/bel_parser/language/function.rb
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- lib/bel_parser/language/quoting.rb
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- lib/bel_parser/language/
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- lib/bel_parser/language/relationship.rb
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- lib/bel_parser/language/semantics.rb
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- lib/bel_parser/language/semantics/analyzer.rb
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- lib/bel_parser/language/semantics/semantic_ast.rb
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- lib/bel_parser/language/semantics/semantic_match.rb
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- lib/bel_parser/language/signature.rb
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- lib/bel_parser/language/specification.rb
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- lib/bel_parser/language/syntax
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- lib/bel_parser/language/version1_0/functions/catalytic_activity.rb
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- lib/bel_parser/language/version1_0/functions/gene_abundance.rb
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- lib/bel_parser/language/version1_0/functions/gtp_bound_activity.rb
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|
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|
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|
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|
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|
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|
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- lib/bel_parser/language/version1_0/relationships/increases.rb
|
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- lib/bel_parser/language/version1_0/relationships/is_a.rb
|
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+
- lib/bel_parser/language/version1_0/relationships/negative_correlation.rb
|
96
|
+
- lib/bel_parser/language/version1_0/relationships/orthologous.rb
|
97
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+
- lib/bel_parser/language/version1_0/relationships/positive_correlation.rb
|
98
|
+
- lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb
|
99
|
+
- lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb
|
100
|
+
- lib/bel_parser/language/version1_0/relationships/reactant_in.rb
|
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+
- lib/bel_parser/language/version1_0/relationships/sub_process_of.rb
|
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+
- lib/bel_parser/language/version1_0/relationships/transcribed_to.rb
|
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+
- lib/bel_parser/language/version1_0/relationships/translated_to.rb
|
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|
+
- lib/bel_parser/language/version1_0/relationships/translocates.rb
|
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+
- lib/bel_parser/language/version1_0/return_types/abundance.rb
|
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+
- lib/bel_parser/language/version1_0/return_types/any.rb
|
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|
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- lib/bel_parser/language/version1_0/return_types/biological_process.rb
|
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- lib/bel_parser/language/version1_0/return_types/catalytic_activity.rb
|
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- lib/bel_parser/language/version1_0/return_types/chaperone_activity.rb
|
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|
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+
- lib/bel_parser/language/version1_0/return_types/fusion.rb
|
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|
+
- lib/bel_parser/language/version1_0/return_types/gene_abundance.rb
|
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+
- lib/bel_parser/language/version1_0/return_types/gtp_bound_activity.rb
|
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+
- lib/bel_parser/language/version1_0/return_types/kinase_activity.rb
|
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|
+
- lib/bel_parser/language/version1_0/return_types/list.rb
|
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|
+
- lib/bel_parser/language/version1_0/return_types/micro_rna_abundance.rb
|
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|
+
- lib/bel_parser/language/version1_0/return_types/molecular_activity.rb
|
118
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+
- lib/bel_parser/language/version1_0/return_types/pathology.rb
|
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+
- lib/bel_parser/language/version1_0/return_types/peptidase_activity.rb
|
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+
- lib/bel_parser/language/version1_0/return_types/phosphatase_activity.rb
|
121
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+
- lib/bel_parser/language/version1_0/return_types/products.rb
|
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+
- lib/bel_parser/language/version1_0/return_types/protein_abundance.rb
|
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+
- lib/bel_parser/language/version1_0/return_types/protein_modification.rb
|
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+
- lib/bel_parser/language/version1_0/return_types/reactants.rb
|
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+
- lib/bel_parser/language/version1_0/return_types/ribosylation_activity.rb
|
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+
- lib/bel_parser/language/version1_0/return_types/rna_abundance.rb
|
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+
- lib/bel_parser/language/version1_0/return_types/substitution.rb
|
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+
- lib/bel_parser/language/version1_0/return_types/transcriptional_activity.rb
|
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+
- lib/bel_parser/language/version1_0/return_types/transport_activity.rb
|
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- lib/bel_parser/language/version1_0/return_types/truncation.rb
|
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+
- lib/bel_parser/language/version1_0/syntax/function.rb
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|
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|
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+
- lib/bel_parser/language/version2_0/functions/activity.rb
|
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+
- lib/bel_parser/language/version2_0/functions/biological_process.rb
|
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+
- lib/bel_parser/language/version2_0/functions/cell_secretion.rb
|
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+
- lib/bel_parser/language/version2_0/functions/cell_surface_expression.rb
|
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+
- lib/bel_parser/language/version2_0/functions/complex_abundance.rb
|
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|
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|
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|
+
- lib/bel_parser/language/version2_0/functions/fragment.rb
|
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|
+
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|
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+
- lib/bel_parser/language/version2_0/functions/fusion.rb
|
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- lib/bel_parser/language/version2_0/functions/gene_abundance.rb
|
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+
- lib/bel_parser/language/version2_0/functions/list.rb
|
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+
- lib/bel_parser/language/version2_0/functions/location.rb
|
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- lib/bel_parser/language/version2_0/functions/micro_rna_abundance.rb
|
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|
+
- lib/bel_parser/language/version2_0/functions/molecular_activity.rb
|
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|
+
- lib/bel_parser/language/version2_0/functions/pathology.rb
|
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|
+
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|
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|
+
- lib/bel_parser/language/version2_0/functions/protein_abundance.rb
|
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|
+
- lib/bel_parser/language/version2_0/functions/protein_modification.rb
|
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+
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|
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|
+
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|
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|
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|
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|
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|
+
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|
158
|
+
- lib/bel_parser/language/version2_0/functions/variant.rb
|
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|
+
- lib/bel_parser/language/version2_0/relationships/acts_in.rb
|
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|
+
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|
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+
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|
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|
+
- lib/bel_parser/language/version2_0/relationships/biomarker_for.rb
|
163
|
+
- lib/bel_parser/language/version2_0/relationships/causes_no_change.rb
|
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+
- lib/bel_parser/language/version2_0/relationships/decreases.rb
|
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- lib/bel_parser/language/version2_0/relationships/directly_decreases.rb
|
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+
- lib/bel_parser/language/version2_0/relationships/directly_increases.rb
|
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|
+
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|
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|
+
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|
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+
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|
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|
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|
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|
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|
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|
+
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|
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+
- lib/bel_parser/language/version2_0/relationships/increases.rb
|
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+
- lib/bel_parser/language/version2_0/relationships/is_a.rb
|
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|
+
- lib/bel_parser/language/version2_0/relationships/negative_correlation.rb
|
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+
- lib/bel_parser/language/version2_0/relationships/orthologous.rb
|
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|
+
- lib/bel_parser/language/version2_0/relationships/positive_correlation.rb
|
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|
+
- lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb
|
181
|
+
- lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb
|
182
|
+
- lib/bel_parser/language/version2_0/relationships/reactant_in.rb
|
183
|
+
- lib/bel_parser/language/version2_0/relationships/regulates.rb
|
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+
- lib/bel_parser/language/version2_0/relationships/sub_process_of.rb
|
185
|
+
- lib/bel_parser/language/version2_0/relationships/transcribed_to.rb
|
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|
+
- lib/bel_parser/language/version2_0/relationships/translated_to.rb
|
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|
+
- lib/bel_parser/language/version2_0/relationships/translocates.rb
|
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+
- lib/bel_parser/language/version2_0/return_types/abundance.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/activity.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/any.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/biological_process.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/complex_abundance.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/fragment.rb
|
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+
- lib/bel_parser/language/version2_0/return_types/from_location.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/fusion.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/gene_abundance.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/list.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/location.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/micro_rna_abundance.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/molecular_activity.rb
|
201
|
+
- lib/bel_parser/language/version2_0/return_types/pathology.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/products.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/protein_abundance.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/protein_modification.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/reactants.rb
|
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|
+
- lib/bel_parser/language/version2_0/return_types/rna_abundance.rb
|
207
|
+
- lib/bel_parser/language/version2_0/return_types/to_location.rb
|
208
|
+
- lib/bel_parser/language/version2_0/return_types/variant.rb
|
148
209
|
- lib/bel_parser/mixin/line_continuator.rb
|
149
210
|
- lib/bel_parser/mixin/line_mapping.rb
|
150
211
|
- lib/bel_parser/parser.rb
|
@@ -1,14 +0,0 @@
|
|
1
|
-
module BELParser
|
2
|
-
module Language
|
3
|
-
module Syntax
|
4
|
-
module Expression
|
5
|
-
# AST traversal observer that reports if any node is incomplete.
|
6
|
-
class IncompleteNode
|
7
|
-
def update(node)
|
8
|
-
"[#{node.type}] Incomplete #{node.type}." if node.incomplete?
|
9
|
-
end
|
10
|
-
end
|
11
|
-
end
|
12
|
-
end
|
13
|
-
end
|
14
|
-
end
|
@@ -1,22 +0,0 @@
|
|
1
|
-
module BELParser
|
2
|
-
module Language
|
3
|
-
module Syntax
|
4
|
-
module Expression
|
5
|
-
# AST traversal observer that reports if term functions are invalid
|
6
|
-
# according to a {BELParser::Language::Specification}.
|
7
|
-
class InvalidTermFunction
|
8
|
-
def initialize(specification)
|
9
|
-
@specification = specification
|
10
|
-
end
|
11
|
-
|
12
|
-
def update(node)
|
13
|
-
return unless node.type == :term
|
14
|
-
function_string = node.children[0].children[0].children[0]
|
15
|
-
msg = "[#{node.type}] Invalid function: #{function_string}"
|
16
|
-
msg unless @specification.function(function_string.to_sym)
|
17
|
-
end
|
18
|
-
end
|
19
|
-
end
|
20
|
-
end
|
21
|
-
end
|
22
|
-
end
|
@@ -1,50 +0,0 @@
|
|
1
|
-
require_relative 'function'
|
2
|
-
require_relative 'specification'
|
3
|
-
|
4
|
-
# Require all version 1.0 return types
|
5
|
-
Dir[
|
6
|
-
File.join(
|
7
|
-
File.dirname(File.expand_path(__FILE__)),
|
8
|
-
'version1', 'return_types', '*.rb')
|
9
|
-
].each do |path|
|
10
|
-
require_relative "version1/return_types/#{File.basename(path)}"
|
11
|
-
end
|
12
|
-
|
13
|
-
# Require all version 1.0 functions.
|
14
|
-
Dir[
|
15
|
-
File.join(
|
16
|
-
File.dirname(File.expand_path(__FILE__)),
|
17
|
-
'version1', 'functions', '*.rb')
|
18
|
-
].each do |path|
|
19
|
-
require_relative "version1/functions/#{File.basename(path)}"
|
20
|
-
end
|
21
|
-
|
22
|
-
module BELParser
|
23
|
-
module Language
|
24
|
-
module Version1
|
25
|
-
# Version1Specification defines the BEL, version 1.0 specification.
|
26
|
-
class Specification
|
27
|
-
include BELParser::Language::Specification
|
28
|
-
def initialize
|
29
|
-
# Establish functions
|
30
|
-
function_classes = Version1::Functions.constants.collect do |symbol|
|
31
|
-
const = Version1::Functions.const_get(symbol)
|
32
|
-
const if
|
33
|
-
const.respond_to?(:short) &&
|
34
|
-
const.respond_to?(:long)
|
35
|
-
end
|
36
|
-
@functions = function_classes.compact
|
37
|
-
@indexed_functions = index_functions(@functions)
|
38
|
-
|
39
|
-
# Establish return types
|
40
|
-
ret_classes = Version1::ReturnTypes.constants.collect do |symbol|
|
41
|
-
const = Version1::ReturnTypes.const_get(symbol)
|
42
|
-
const if const.respond_to?(:subtypes)
|
43
|
-
end
|
44
|
-
@return_types = ret_classes.compact
|
45
|
-
@indexed_return_types = index_return_types(@return_types)
|
46
|
-
end
|
47
|
-
end
|
48
|
-
end
|
49
|
-
end
|
50
|
-
end
|
@@ -1,50 +0,0 @@
|
|
1
|
-
require_relative 'function'
|
2
|
-
require_relative 'specification'
|
3
|
-
|
4
|
-
# Require all version 2.0 return types
|
5
|
-
Dir[
|
6
|
-
File.join(
|
7
|
-
File.dirname(File.expand_path(__FILE__)),
|
8
|
-
'version2', 'return_types', '*.rb')
|
9
|
-
].each do |path|
|
10
|
-
require_relative "version2/return_types/#{File.basename(path)}"
|
11
|
-
end
|
12
|
-
|
13
|
-
# Require all version 2.0 functions.
|
14
|
-
Dir[
|
15
|
-
File.join(
|
16
|
-
File.dirname(File.expand_path(__FILE__)),
|
17
|
-
'version2', 'functions', '*.rb')
|
18
|
-
].each do |path|
|
19
|
-
require_relative "version2/functions/#{File.basename(path)}"
|
20
|
-
end
|
21
|
-
|
22
|
-
module BELParser
|
23
|
-
module Language
|
24
|
-
module Version2
|
25
|
-
# Version2Specification defines the BEL, version 2.0 specification.
|
26
|
-
class Specification
|
27
|
-
include BELParser::Language::Specification
|
28
|
-
def initialize
|
29
|
-
# Establish functions
|
30
|
-
function_classes = Version2::Functions.constants.collect do |symbol|
|
31
|
-
const = Version2::Functions.const_get(symbol)
|
32
|
-
const if
|
33
|
-
const.respond_to?(:short) &&
|
34
|
-
const.respond_to?(:long)
|
35
|
-
end
|
36
|
-
@functions = function_classes.compact
|
37
|
-
@indexed_functions = index_functions(@functions)
|
38
|
-
|
39
|
-
# Establish return types
|
40
|
-
ret_classes = Version2::ReturnTypes.constants.collect do |symbol|
|
41
|
-
const = Version2::ReturnTypes.const_get(symbol)
|
42
|
-
const if const.respond_to?(:subtypes)
|
43
|
-
end
|
44
|
-
@return_types = ret_classes.compact
|
45
|
-
@indexed_return_types = index_return_types(@return_types)
|
46
|
-
end
|
47
|
-
end
|
48
|
-
end
|
49
|
-
end
|
50
|
-
end
|