bel_parser 1.1.2-java → 1.1.3-java

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data/CHANGELOG.md CHANGED
@@ -8,3 +8,6 @@ This project adheres to [Semantic Versioning](http://semver.org/).
8
8
  ### Added
9
9
 
10
10
  [1.0.0]: https://github.com/OpenBEL/bel_parser/compare/0.0.0...1.0.0
11
+
12
+ [1.1.3]: https://github.com/OpenBEL/bel_parser/compare/1.0.0...1.1.3
13
+
data/VERSION CHANGED
@@ -1 +1 @@
1
- 1.1.2
1
+ 1.1.3
data/bin/bel2_validator CHANGED
@@ -87,7 +87,11 @@ uri_reader, url_reader = options.values_at(:uri_reader, :url_reader)
87
87
  namespaces = Hash[
88
88
  ARGV.map do |ns|
89
89
  keyword, identifier = ns.split('=')
90
- [keyword, BELParser::Expression::Model::Namespace.new(keyword, identifier, nil)]
90
+ if identifier.end_with?('.belns')
91
+ [keyword, BELParser::Expression::Model::Namespace.new(keyword, nil, identifier)]
92
+ else
93
+ [keyword, BELParser::Expression::Model::Namespace.new(keyword, identifier, nil)]
94
+ end
91
95
  end.compact
92
96
  ]
93
97
 
@@ -81,7 +81,11 @@ url_reader = options[:url_reader]
81
81
  namespaces = Hash[
82
82
  ARGV.map do |ns|
83
83
  keyword, identifier = ns.split('=')
84
- [keyword, BELParser::Expression::Model::Namespace.new(keyword, identifier, nil)]
84
+ if identifier.end_with?('.belns')
85
+ [keyword, BELParser::Expression::Model::Namespace.new(keyword, nil, identifier)]
86
+ else
87
+ [keyword, BELParser::Expression::Model::Namespace.new(keyword, identifier, nil)]
88
+ end
85
89
  end.compact
86
90
  ]
87
91
 
@@ -0,0 +1,48 @@
1
+ require 'bel_parser/language/term_transformation'
2
+
3
+ module BELParser
4
+ module Language
5
+ # ApplyDefaultNamespace sets the DEFAULT namespace for values when one is
6
+ # not provided. Applies to all namespace values within a BEL 2.0 expression.
7
+ class ApplyDefaultNamespace
8
+ include BELParser::Language::TermTransformation
9
+
10
+ def initialize(language_spec, namespace_hash, uri_reader, url_reader)
11
+ @language_spec = language_spec
12
+ @namespace_hash = namespace_hash
13
+ @uri_reader = uri_reader
14
+ @url_reader = url_reader
15
+ end
16
+
17
+ def on_term(term_node)
18
+ term_node.updated([
19
+ term_node.function,
20
+ term_node.arguments.map! {|arg| argument(process(arg.child))}
21
+ ].flatten)
22
+ end
23
+
24
+ def on_argument(argument_node)
25
+ process(argument_node.child)
26
+ end
27
+
28
+ def on_parameter(parameter_node)
29
+ parameter_node.updated([
30
+ process(parameter_node.prefix),
31
+ parameter_node.value
32
+ ].flatten)
33
+ end
34
+
35
+ def on_prefix(prefix_node)
36
+ # guard: return prefix AST node if namespace already supplied
37
+ return prefix_node if prefix_node.identifier
38
+
39
+ # return "DEFAULT" namespace
40
+ prefix(
41
+ identifier(
42
+ 'DEFAULT',
43
+ :complete => true),
44
+ :complete => true)
45
+ end
46
+ end
47
+ end
48
+ end
@@ -1,5 +1,6 @@
1
1
  require_relative 'syntax'
2
2
  require_relative 'semantics'
3
+ require_relative 'apply_default_namespace'
3
4
  require_relative 'apply_namespace_encoding'
4
5
 
5
6
  module BELParser
@@ -9,11 +10,13 @@ module BELParser
9
10
  # namespaces.
10
11
  class ExpressionValidator
11
12
  def initialize(spec, namespaces, uri_reader, url_reader)
12
- @spec = spec
13
- @namespaces = namespaces || {}
14
- @syntax_functions = Syntax.syntax_functions
15
- @semantics_functions = Semantics.semantics_functions
16
- @transform =
13
+ @spec = spec
14
+ @namespaces = namespaces || {}
15
+ @syntax_functions = Syntax.syntax_functions
16
+ @semantics_functions = Semantics.semantics_functions
17
+ @default_namespace_transform =
18
+ ApplyDefaultNamespace.new(@spec, @namespaces, uri_reader, url_reader)
19
+ @namespace_encoding_transform =
17
20
  ApplyNamespaceEncoding.new(@spec, @namespaces, uri_reader, url_reader)
18
21
  end
19
22
 
@@ -23,7 +26,11 @@ module BELParser
23
26
  # @param [BELParser::Parsers::AST::Node] expression_node to validate
24
27
  # @return [BELParser::Language::Syntax::SyntaxResult] syntax results
25
28
  def validate(expression_node)
26
- @transform.process(expression_node)
29
+ if @spec.version >= "2.0"
30
+ expression_node = @default_namespace_transform.process(expression_node)
31
+ end
32
+
33
+ @namespace_encoding_transform.process(expression_node)
27
34
 
28
35
  case expression_node
29
36
  when BELParser::Parsers::AST::SimpleStatement
@@ -574,7 +574,7 @@ module BELParser
574
574
  unless prefix_node.respond_to?(:namespace) && prefix_node.namespace
575
575
  return invalid_namespace(prefix_node, spec, namespaces)
576
576
  end
577
-
577
+
578
578
  if namespaces.any? { |i| i == :* || i == input_namespace }
579
579
  success(prefix_node, spec)
580
580
  else
@@ -736,8 +736,16 @@ module BELParser
736
736
  end
737
737
 
738
738
  def match(value_node, spec)
739
- string_literal = value_node.children[0]
740
- case string_literal
739
+ ident_or_string = value_node.children[0]
740
+ value =
741
+ case ident_or_string
742
+ when BELParser::Parsers::AST::String
743
+ ident_or_string.string_value
744
+ else
745
+ ident_or_string.string_literal
746
+ end
747
+
748
+ case value
741
749
  when START_STOP, UNDETERMINED, UNKNOWN_START_STOP
742
750
  success(value_node, spec)
743
751
  else
@@ -70,6 +70,35 @@ module BELParser
70
70
  end
71
71
  end
72
72
 
73
+ class FragmentWithAnySignature
74
+ extend BELParser::Language::Signature
75
+
76
+ private_class_method :new
77
+
78
+ AST = BELParser::Language::Semantics::Builder.build do
79
+ term(
80
+ function(
81
+ identifier(
82
+ function_of(Fragment))),
83
+ argument(
84
+ parameter(
85
+ prefix(any),
86
+ value(any))))
87
+ end
88
+ private_constant :AST
89
+
90
+ STRING_FORM = 'fragment(E:*)abundance'.freeze
91
+ private_constant :STRING_FORM
92
+
93
+ def self.semantic_ast
94
+ AST
95
+ end
96
+
97
+ def self.string_form
98
+ STRING_FORM
99
+ end
100
+ end
101
+
73
102
  # FragmentWithRangeDescriptorSignature
74
103
  class FragmentWithRangeDescriptorSignature
75
104
  extend BELParser::Language::Signature
@@ -104,6 +133,41 @@ module BELParser
104
133
  STRING_FORM
105
134
  end
106
135
  end
136
+
137
+ # FragmentWithRangeDescriptorSignature
138
+ class FragmentWithAnyDescriptorSignature
139
+ extend BELParser::Language::Signature
140
+
141
+ private_class_method :new
142
+
143
+ AST = BELParser::Language::Semantics::Builder.build do
144
+ term(
145
+ function(
146
+ identifier(
147
+ function_of(Fragment))),
148
+ argument(
149
+ parameter(
150
+ prefix(any),
151
+ value(any))),
152
+ argument(
153
+ parameter(
154
+ prefix(any),
155
+ value(any))))
156
+ end
157
+ private_constant :AST
158
+
159
+ STRING_FORM = 'fragment(E:*,E:*)abundance'.freeze
160
+ private_constant :STRING_FORM
161
+
162
+ def self.semantic_ast
163
+ AST
164
+ end
165
+
166
+ def self.string_form
167
+ STRING_FORM
168
+ end
169
+ end
170
+
107
171
  end
108
172
 
109
173
  SIGNATURES = Signatures.constants.map do |const|
@@ -15,7 +15,7 @@ module BELParser
15
15
  SHORT = :fromLoc
16
16
  LONG = :fromLocation
17
17
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::FromLocation
18
- L_ENC = Version2_0::ValueEncodings::Location
18
+ A_ENC = Version2_0::ValueEncodings::Abundance
19
19
  DESCRIPTION = 'Denotes the from cellular location of the
20
20
  abundance.'.freeze
21
21
 
@@ -58,7 +58,7 @@ module BELParser
58
58
  namespace_of(:*)),
59
59
  value(
60
60
  has_encoding,
61
- encoding_of(L_ENC)))))
61
+ encoding_of(A_ENC)))))
62
62
  end
63
63
  private_constant :AST
64
64
 
@@ -73,6 +73,36 @@ module BELParser
73
73
  STRING_FORM
74
74
  end
75
75
  end
76
+
77
+ class FromLocationAnySignature
78
+ extend BELParser::Language::Signature
79
+
80
+ private_class_method :new
81
+
82
+ AST = BELParser::Language::Semantics::Builder.build do
83
+ term(
84
+ function(
85
+ identifier(
86
+ function_of(FromLocation))),
87
+ argument(
88
+ parameter(
89
+ prefix(any),
90
+ value(any))))
91
+ end
92
+ private_constant :AST
93
+
94
+ STRING_FORM = 'fromLocation(Any)fromLocation'.freeze
95
+ private_constant :STRING_FORM
96
+
97
+ def self.semantic_ast
98
+ AST
99
+ end
100
+
101
+ def self.string_form
102
+ STRING_FORM
103
+ end
104
+ end
105
+
76
106
  end
77
107
 
78
108
  SIGNATURES = Signatures.constants.map do |const|
@@ -14,7 +14,7 @@ module BELParser
14
14
  SHORT = :loc
15
15
  LONG = :location
16
16
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Location
17
- L_ENC = Version2_0::ValueEncodings::Location
17
+ A_ENC = Version2_0::ValueEncodings::Abundance
18
18
  DESCRIPTION = 'Denotes the cellular location of the abundance.'.freeze
19
19
 
20
20
  def self.short
@@ -56,7 +56,7 @@ module BELParser
56
56
  namespace_of(:*)),
57
57
  value(
58
58
  has_encoding,
59
- encoding_of(L_ENC)))))
59
+ encoding_of(A_ENC)))))
60
60
  end
61
61
  private_constant :AST
62
62
 
@@ -71,6 +71,39 @@ module BELParser
71
71
  STRING_FORM
72
72
  end
73
73
  end
74
+
75
+ # LocationSignature
76
+ class LocationAnySignature
77
+ extend BELParser::Language::Signature
78
+
79
+ private_class_method :new
80
+
81
+ AST = BELParser::Language::Semantics::Builder.build do
82
+ term(
83
+ function(
84
+ identifier(
85
+ function_of(Location))),
86
+ argument(
87
+ parameter(
88
+ prefix(
89
+ has_namespace,
90
+ namespace_of(:*)),
91
+ value(any))))
92
+ end
93
+ private_constant :AST
94
+
95
+ STRING_FORM = 'location(Any)location'.freeze
96
+ private_constant :STRING_FORM
97
+
98
+ def self.semantic_ast
99
+ AST
100
+ end
101
+
102
+ def self.string_form
103
+ STRING_FORM
104
+ end
105
+ end
106
+
74
107
  end
75
108
 
76
109
  SIGNATURES = Signatures.constants.map do |const|
@@ -74,8 +74,37 @@ module BELParser
74
74
  STRING_FORM
75
75
  end
76
76
  end
77
- end
78
77
 
78
+ # MolecularActivitySignature
79
+ class MolecularActivityAnySignature
80
+ extend BELParser::Language::Signature
81
+
82
+ private_class_method :new
83
+
84
+ AST = BELParser::Language::Semantics::Builder.build do
85
+ term(
86
+ function(
87
+ identifier(
88
+ function_of(MolecularActivity))),
89
+ argument(
90
+ parameter(
91
+ prefix(any),
92
+ value(any))))
93
+ end
94
+ private_constant :AST
95
+
96
+ STRING_FORM = 'molecularActivity(Any)molecularActivity'.freeze
97
+ private_constant :STRING_FORM
98
+
99
+ def self.semantic_ast
100
+ AST
101
+ end
102
+
103
+ def self.string_form
104
+ STRING_FORM
105
+ end
106
+ end
107
+ end
79
108
  SIGNATURES = Signatures.constants.map do |const|
80
109
  Signatures.const_get(const)
81
110
  end.freeze
@@ -55,9 +55,10 @@ module BELParser
55
55
  argument(
56
56
  parameter(
57
57
  prefix(any),
58
- value(
59
- has_encoding,
60
- encoding_of(E_ENC)))))
58
+ value(any))))
59
+ # value(
60
+ # has_encoding,
61
+ # encoding_of(E_ENC)))))
61
62
  end
62
63
  private_constant :AST
63
64
 
@@ -90,9 +91,10 @@ module BELParser
90
91
  argument(
91
92
  parameter(
92
93
  prefix(any),
93
- value(
94
- has_encoding,
95
- encoding_of(E_ENC)))),
94
+ value(any))),
95
+ # value(
96
+ # has_encoding,
97
+ # encoding_of(E_ENC)))),
96
98
  argument(
97
99
  parameter(
98
100
  prefix(any),
@@ -130,9 +132,10 @@ module BELParser
130
132
  argument(
131
133
  parameter(
132
134
  prefix(any),
133
- value(
134
- has_encoding,
135
- encoding_of(E_ENC)))),
135
+ value(any))),
136
+ # value(
137
+ # has_encoding,
138
+ # encoding_of(E_ENC)))),
136
139
  argument(
137
140
  parameter(
138
141
  prefix(any),
@@ -13,7 +13,7 @@ module BELParser
13
13
 
14
14
  SHORT = :r
15
15
  LONG = :rnaAbundance
16
- RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::GeneAbundance
16
+ RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::RNAAbundance
17
17
  R_ENC = Version2_0::ValueEncodings::RNAAbundance
18
18
  DESCRIPTION = 'Denotes the abundance of a gene'.freeze
19
19
 
@@ -14,7 +14,7 @@ module BELParser
14
14
  SHORT = :toLoc
15
15
  LONG = :toLocation
16
16
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ToLocation
17
- L_ENC = Version2_0::ValueEncodings::Location
17
+ A_ENC = Version2_0::ValueEncodings::Abundance
18
18
  DESCRIPTION = 'Denotes the to cellular location of the
19
19
  abundance.'.freeze
20
20
 
@@ -57,7 +57,7 @@ module BELParser
57
57
  namespace_of(:*)),
58
58
  value(
59
59
  has_encoding,
60
- encoding_of(L_ENC)))))
60
+ encoding_of(A_ENC)))))
61
61
  end
62
62
  private_constant :AST
63
63
 
@@ -72,6 +72,37 @@ module BELParser
72
72
  STRING_FORM
73
73
  end
74
74
  end
75
+
76
+ # ToLocationAnySignature
77
+ class ToLocationAnySignature
78
+ extend BELParser::Language::Signature
79
+
80
+ private_class_method :new
81
+
82
+ AST = BELParser::Language::Semantics::Builder.build do
83
+ term(
84
+ function(
85
+ identifier(
86
+ function_of(ToLocation))),
87
+ argument(
88
+ parameter(
89
+ prefix(any),
90
+ value(any))))
91
+ end
92
+ private_constant :AST
93
+
94
+ STRING_FORM = 'toLocation(Any)toLocation'.freeze
95
+ private_constant :STRING_FORM
96
+
97
+ def self.semantic_ast
98
+ AST
99
+ end
100
+
101
+ def self.string_form
102
+ STRING_FORM
103
+ end
104
+ end
105
+
75
106
  end
76
107
 
77
108
  SIGNATURES = Signatures.constants.map do |const|
@@ -5,7 +5,7 @@ module BELParser
5
5
  module Version2_0
6
6
  module ValueEncodings
7
7
  # Location value encoding.
8
- class Location < Any
8
+ class Location < Abundance
9
9
  # Return the {Symbol} value.
10
10
  #
11
11
  # @note This method should be overridden in subclasses.
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bel_parser
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.1.2
4
+ version: 1.1.3
5
5
  platform: java
6
6
  authors:
7
7
  - Anthony Bargnesi
@@ -56,11 +56,11 @@ dependencies:
56
56
  description: Implements language versions 1.0 and 2.0.
57
57
  email: abargnesi@selventa.com
58
58
  executables:
59
+ - bel2_compatibility
60
+ - bel2_debug_ast
59
61
  - bel2_upgrade
60
62
  - bel2_validator
61
63
  - bel_script_reader
62
- - bel2_compatibility
63
- - bel2_debug_ast
64
64
  extensions: []
65
65
  extra_rdoc_files: []
66
66
  files:
@@ -98,6 +98,7 @@ files:
98
98
  - lib/bel_parser/expression/validator.rb
99
99
  - lib/bel_parser/language.rb
100
100
  - lib/bel_parser/language/amino_acid.rb
101
+ - lib/bel_parser/language/apply_default_namespace.rb
101
102
  - lib/bel_parser/language/apply_namespace_encoding.rb
102
103
  - lib/bel_parser/language/base_specification.rb
103
104
  - lib/bel_parser/language/covalent_protein_modification.rb
@@ -443,7 +444,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
443
444
  version: '0'
444
445
  requirements: []
445
446
  rubyforge_project:
446
- rubygems_version: 2.6.8
447
+ rubygems_version: 2.4.8
447
448
  signing_key:
448
449
  specification_version: 4
449
450
  summary: Parser for Biolgical Expression Language.