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
@@ -0,0 +1,97 @@
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# begin: ragel
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=begin
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%%{
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machine bel;
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include 'set.rl';
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DOCUMENT_KW = [dD][oO][cC][uU][mM][eE][nN][tT];
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action yield_document_property {
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yield(
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document_property(
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*@buffers[:set].children))
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}
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set_document :=
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SET_KW %set_keyword
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SP+
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DOCUMENT_KW
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SP+
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IDENT %name
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SP+
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EQL
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SP+
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(
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STRING %string_value |
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LIST %list_value |
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IDENT %ident_value
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) NL @yield_document_property;
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}%%
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=end
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# end: ragel
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require_relative '../ast/node'
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require_relative '../mixin/buffer'
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require_relative '../nonblocking_io_wrapper'
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module BELParser
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module Parsers
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module BELScript
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module SetDocument
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class << self
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MAX_LENGTH = 1024 * 128 # 128K
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def parse(content)
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return nil unless content
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Parser.new(content).each do |obj|
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yield obj
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end
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end
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end
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private
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class Parser
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include Enumerable
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include BELParser::Parsers::Buffer
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include BELParser::Parsers::AST::Sexp
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def initialize(content)
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@content = content
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# begin: ragel
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%% write data;
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# end: ragel
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end
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def each
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@buffers = {}
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data = @content.unpack('C*')
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p = 0
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pe = data.length
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eof = data.length
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# begin: ragel
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%% write init;
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%% write exec;
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# end: ragel
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end
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end
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end
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end
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end
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end
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if __FILE__ == $0
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$stdin.each_line do |line|
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BELParser::Parsers::BELScript::SetDocument.parse(line) { |obj|
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puts obj.inspect
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}
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end
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end
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# vim: ft=ruby ts=2 sw=2:
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# encoding: utf-8
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
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name: bel_parser
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3
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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.8
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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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9
9
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autorequire:
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10
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bindir: bin
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11
11
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cert_chain: []
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-
date: 2016-04-
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+
date: 2016-04-13 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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@@ -35,6 +35,10 @@ files:
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35
35
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- lib/bel_parser/language/quoting.rb
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36
36
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- lib/bel_parser/language/relationship.rb
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37
37
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- lib/bel_parser/language/semantics.rb
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38
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+
- lib/bel_parser/language/semantics/deeply_nested_statement.rb
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39
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- lib/bel_parser/language/semantics/function_deprecation.rb
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40
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+
- lib/bel_parser/language/semantics/list_function_subject.rb
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41
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- lib/bel_parser/language/semantics/relationship_deprecation.rb
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38
42
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- lib/bel_parser/language/semantics/signature_mapping.rb
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39
43
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- lib/bel_parser/language/semantics_ast.rb
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40
44
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- lib/bel_parser/language/semantics_function.rb
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@@ -227,6 +231,8 @@ files:
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231
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- lib/bel_parser/parsers/bel_script/define_namespace.rl
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228
232
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- lib/bel_parser/parsers/bel_script/set.rb
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- lib/bel_parser/parsers/bel_script/set.rl
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- lib/bel_parser/parsers/bel_script/set_document.rb
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- lib/bel_parser/parsers/bel_script/set_document.rl
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- lib/bel_parser/parsers/bel_script/unset.rb
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- lib/bel_parser/parsers/bel_script/unset.rl
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- lib/bel_parser/parsers/common.rb
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