bel_parser 1.0.0.alpha.12 → 1.0.0.alpha.13

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (92) hide show
  1. checksums.yaml +4 -4
  2. data/.gemspec +1 -1
  3. data/VERSION +1 -1
  4. data/bin/bel2_validator +35 -8
  5. data/lib/bel_parser/expression/validator.rb +3 -2
  6. data/lib/bel_parser/language/apply_namespace_encoding.rb +96 -0
  7. data/lib/bel_parser/language/base_specification.rb +82 -0
  8. data/lib/bel_parser/language/expression_validator.rb +6 -2
  9. data/lib/bel_parser/language/relationship.rb +1 -1
  10. data/lib/bel_parser/language/semantics/signature_mapping.rb +26 -32
  11. data/lib/bel_parser/language/semantics_ast.rb +285 -149
  12. data/lib/bel_parser/language/semantics_ast_warnings.rb +180 -0
  13. data/lib/bel_parser/language/semantics_result.rb +11 -2
  14. data/lib/bel_parser/language/semantics_type_warning.rb +22 -0
  15. data/lib/bel_parser/language/semantics_warning.rb +8 -0
  16. data/lib/bel_parser/language/specification.rb +38 -55
  17. data/lib/bel_parser/language/syntax/undefined_namespace_value.rb +43 -0
  18. data/lib/bel_parser/language/syntax_error.rb +8 -0
  19. data/lib/bel_parser/language/syntax_result.rb +8 -0
  20. data/lib/bel_parser/language/syntax_warning.rb +9 -4
  21. data/lib/bel_parser/language/version1_0/functions/abundance.rb +5 -6
  22. data/lib/bel_parser/language/version1_0/functions/biological_process.rb +5 -6
  23. data/lib/bel_parser/language/version1_0/functions/complex_abundance.rb +6 -7
  24. data/lib/bel_parser/language/version1_0/functions/fusion.rb +39 -60
  25. data/lib/bel_parser/language/version1_0/functions/gene_abundance.rb +9 -12
  26. data/lib/bel_parser/language/version1_0/functions/list.rb +5 -6
  27. data/lib/bel_parser/language/version1_0/functions/micro_rna_abundance.rb +5 -6
  28. data/lib/bel_parser/language/version1_0/functions/pathology.rb +5 -6
  29. data/lib/bel_parser/language/version1_0/functions/protein_abundance.rb +16 -30
  30. data/lib/bel_parser/language/version1_0/functions/protein_modification.rb +15 -27
  31. data/lib/bel_parser/language/version1_0/functions/rna_abundance.rb +8 -11
  32. data/lib/bel_parser/language/version1_0/functions/substitution.rb +6 -12
  33. data/lib/bel_parser/language/version1_0/functions/translocation.rb +9 -12
  34. data/lib/bel_parser/language/version1_0/functions/truncation.rb +2 -4
  35. data/lib/bel_parser/language/version1_0/value_encodings/abundance.rb +21 -0
  36. data/lib/bel_parser/language/version1_0/value_encodings/any.rb +74 -0
  37. data/lib/bel_parser/language/version1_0/value_encodings/biological_process.rb +21 -0
  38. data/lib/bel_parser/language/version1_0/value_encodings/complex_abundance.rb +21 -0
  39. data/lib/bel_parser/language/version1_0/value_encodings/gene_abundance.rb +21 -0
  40. data/lib/bel_parser/language/version1_0/value_encodings/micro_rna_abundance.rb +21 -0
  41. data/lib/bel_parser/language/version1_0/value_encodings/pathology.rb +21 -0
  42. data/lib/bel_parser/language/version1_0/value_encodings/protein_abundance.rb +21 -0
  43. data/lib/bel_parser/language/version1_0/value_encodings/rna_abundance.rb +21 -0
  44. data/lib/bel_parser/language/version1_0.rb +6 -87
  45. data/lib/bel_parser/language/version2_0/functions/abundance.rb +13 -18
  46. data/lib/bel_parser/language/version2_0/functions/biological_process.rb +5 -6
  47. data/lib/bel_parser/language/version2_0/functions/complex_abundance.rb +9 -12
  48. data/lib/bel_parser/language/version2_0/functions/fragment.rb +4 -9
  49. data/lib/bel_parser/language/version2_0/functions/from_location.rb +5 -6
  50. data/lib/bel_parser/language/version2_0/functions/fusion.rb +39 -66
  51. data/lib/bel_parser/language/version2_0/functions/gene_abundance.rb +13 -18
  52. data/lib/bel_parser/language/version2_0/functions/list.rb +5 -6
  53. data/lib/bel_parser/language/version2_0/functions/location.rb +5 -6
  54. data/lib/bel_parser/language/version2_0/functions/micro_rna_abundance.rb +13 -18
  55. data/lib/bel_parser/language/version2_0/functions/molecular_activity.rb +6 -5
  56. data/lib/bel_parser/language/version2_0/functions/pathology.rb +5 -6
  57. data/lib/bel_parser/language/version2_0/functions/protein_abundance.rb +21 -30
  58. data/lib/bel_parser/language/version2_0/functions/protein_modification.rb +11 -17
  59. data/lib/bel_parser/language/version2_0/functions/rna_abundance.rb +13 -18
  60. data/lib/bel_parser/language/version2_0/functions/to_location.rb +5 -6
  61. data/lib/bel_parser/language/version2_0/functions/variant.rb +1 -4
  62. data/lib/bel_parser/language/version2_0/value_encodings/abundance.rb +21 -0
  63. data/lib/bel_parser/language/version2_0/value_encodings/activity.rb +21 -0
  64. data/lib/bel_parser/language/version2_0/value_encodings/any.rb +74 -0
  65. data/lib/bel_parser/language/version2_0/value_encodings/biological_process.rb +21 -0
  66. data/lib/bel_parser/language/version2_0/value_encodings/complex_abundance.rb +21 -0
  67. data/lib/bel_parser/language/version2_0/value_encodings/gene_abundance.rb +21 -0
  68. data/lib/bel_parser/language/version2_0/value_encodings/location.rb +21 -0
  69. data/lib/bel_parser/language/version2_0/value_encodings/micro_rna_abundance.rb +21 -0
  70. data/lib/bel_parser/language/version2_0/value_encodings/pathology.rb +21 -0
  71. data/lib/bel_parser/language/version2_0/value_encodings/protein_abundance.rb +21 -0
  72. data/lib/bel_parser/language/version2_0/value_encodings/protein_modification.rb +21 -0
  73. data/lib/bel_parser/language/version2_0/value_encodings/rna_abundance.rb +21 -0
  74. data/lib/bel_parser/language/version2_0.rb +6 -60
  75. data/lib/bel_parser/language.rb +3 -4
  76. data/lib/bel_parser/parsers/ast/node.rb +14 -2
  77. data/lib/bel_parser/{language/quoting.rb → quoting.rb} +0 -56
  78. data/lib/bel_parser/resource/concept.rb +56 -0
  79. data/lib/bel_parser/resource/concept_scheme.rb +35 -0
  80. data/lib/bel_parser/resource/dataset.rb +34 -0
  81. data/lib/bel_parser/resource/eager_reader.rb +75 -0
  82. data/lib/bel_parser/resource/eager_sparql_reader.rb +51 -0
  83. data/lib/bel_parser/resource/http_cache.rb +71 -0
  84. data/lib/bel_parser/resource/jena_tdb_reader.rb +246 -0
  85. data/lib/bel_parser/resource/lru_cache.rb +111 -0
  86. data/lib/bel_parser/resource/lru_reader.rb +38 -0
  87. data/lib/bel_parser/resource/reader.rb +18 -0
  88. data/lib/bel_parser/resource/resource_file_reader.rb +134 -0
  89. data/lib/bel_parser/resource/sparql_reader.rb +178 -0
  90. data/lib/bel_parser/resource/value.rb +31 -0
  91. metadata +42 -4
  92. data/lib/bel_parser/language/version1_0/syntax/function.rb +0 -28
data/lib/bel_parser/language/version2_0/functions/fusion.rb CHANGED
@@ -15,6 +15,9 @@ module BELParser
15
15
  SHORT = :fus
16
16
  LONG = :fusion
17
17
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Fusion
18
+ G_ENC = Version2_0::ValueEncodings::GeneAbundance
19
+ P_ENC = Version2_0::ValueEncodings::ProteinAbundance
20
+ R_ENC = Version2_0::ValueEncodings::RNAAbundance
18
21
  DESCRIPTION = 'Specifies the abundance of a protein translated
19
22
  rom the fusion of a gene.'.freeze
20
23
 
@@ -53,37 +56,27 @@ module BELParser
53
56
  argument(
54
57
  parameter(
55
58
  prefix(
56
- identifier(
57
- has_namespace,
58
- namespace_of(:*))),
59
+ has_namespace,
60
+ namespace_of(:*)),
59
61
  value(
60
- value_type(
61
- has_encoding,
62
- encoding_of(:GeneAbundance))))),
62
+ has_encoding,
63
+ encoding_of(G_ENC)))),
63
64
  argument(
64
65
  parameter(
65
- prefix(
66
- any),
67
- value(
68
- value_type(
69
- encoding_of(:*))))),
66
+ prefix(any),
67
+ value(any))),
70
68
  argument(
71
69
  parameter(
72
70
  prefix(
73
- identifier(
74
- has_namespace,
75
- namespace_of(:*))),
71
+ has_namespace,
72
+ namespace_of(:*)),
76
73
  value(
77
- value_type(
78
- has_encoding,
79
- encoding_of(:GeneAbundance))))),
74
+ has_encoding,
75
+ encoding_of(G_ENC)))),
80
76
  argument(
81
77
  parameter(
82
- prefix(
83
- any),
84
- value(
85
- value_type(
86
- encoding_of(:*))))))
78
+ prefix(any),
79
+ value(any))))
87
80
  end
88
81
  private_constant :AST
89
82
 
@@ -113,37 +106,27 @@ module BELParser
113
106
  argument(
114
107
  parameter(
115
108
  prefix(
116
- identifier(
117
- has_namespace,
118
- namespace_of(:*))),
109
+ has_namespace,
110
+ namespace_of(:*)),
119
111
  value(
120
- value_type(
121
- has_encoding,
122
- encoding_of(:ProteinAbundance))))),
112
+ has_encoding,
113
+ encoding_of(P_ENC)))),
123
114
  argument(
124
115
  parameter(
125
- prefix(
126
- any),
127
- value(
128
- value_type(
129
- encoding_of(:*))))),
116
+ prefix(any),
117
+ value(any))),
130
118
  argument(
131
119
  parameter(
132
120
  prefix(
133
- identifier(
134
- has_namespace,
135
- namespace_of(:*))),
121
+ has_namespace,
122
+ namespace_of(:*)),
136
123
  value(
137
- value_type(
138
- has_encoding,
139
- encoding_of(:ProteinAbundance))))),
124
+ has_encoding,
125
+ encoding_of(P_ENC)))),
140
126
  argument(
141
127
  parameter(
142
- prefix(
143
- any),
144
- value(
145
- value_type(
146
- encoding_of(:*))))))
128
+ prefix(any),
129
+ value(any))))
147
130
  end
148
131
  private_constant :AST
149
132
 
@@ -173,37 +156,27 @@ module BELParser
173
156
  argument(
174
157
  parameter(
175
158
  prefix(
176
- identifier(
177
- has_namespace,
178
- namespace_of(:*))),
159
+ has_namespace,
160
+ namespace_of(:*)),
179
161
  value(
180
- value_type(
181
- has_encoding,
182
- encoding_of(:RnaAbundance))))),
162
+ has_encoding,
163
+ encoding_of(R_ENC)))),
183
164
  argument(
184
165
  parameter(
185
- prefix(
186
- any),
187
- value(
188
- value_type(
189
- encoding_of(:*))))),
166
+ prefix(any),
167
+ value(any))),
190
168
  argument(
191
169
  parameter(
192
170
  prefix(
193
- identifier(
194
- has_namespace,
195
- namespace_of(:*))),
171
+ has_namespace,
172
+ namespace_of(:*)),
196
173
  value(
197
- value_type(
198
- has_encoding,
199
- encoding_of(:RnaAbundance))))),
174
+ has_encoding,
175
+ encoding_of(R_ENC)))),
200
176
  argument(
201
177
  parameter(
202
- prefix(
203
- any),
204
- value(
205
- value_type(
206
- encoding_of(:*))))))
178
+ prefix(any),
179
+ value(any))))
207
180
  end
208
181
  private_constant :AST
209
182
 
data/lib/bel_parser/language/version2_0/functions/gene_abundance.rb CHANGED
@@ -14,6 +14,7 @@ module BELParser
14
14
  SHORT = :g
15
15
  LONG = :geneAbundance
16
16
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::GeneAbundance
17
+ G_ENC = Version2_0::ValueEncodings::GeneAbundance
17
18
  DESCRIPTION = 'Denotes the abundance of a gene.'.freeze
18
19
 
19
20
  def self.short
@@ -51,13 +52,11 @@ module BELParser
51
52
  argument(
52
53
  parameter(
53
54
  prefix(
54
- identifier(
55
- has_namespace,
56
- namespace_of(:*))),
55
+ has_namespace,
56
+ namespace_of(:*)),
57
57
  value(
58
- value_type(
59
- has_encoding,
60
- encoding_of(:GeneAbundance))))))
58
+ has_encoding,
59
+ encoding_of(G_ENC)))))
61
60
  end
62
61
  private_constant :AST
63
62
 
@@ -118,13 +117,11 @@ module BELParser
118
117
  argument(
119
118
  parameter(
120
119
  prefix(
121
- identifier(
122
- has_namespace,
123
- namespace_of(:*))),
120
+ has_namespace,
121
+ namespace_of(:*)),
124
122
  value(
125
- value_type(
126
- has_encoding,
127
- encoding_of(:Abundance))))),
123
+ has_encoding,
124
+ encoding_of(G_ENC)))),
128
125
  argument(
129
126
  term(
130
127
  function(
@@ -159,13 +156,11 @@ module BELParser
159
156
  argument(
160
157
  parameter(
161
158
  prefix(
162
- identifier(
163
- has_namespace,
164
- namespace_of(:*))),
159
+ has_namespace,
160
+ namespace_of(:*)),
165
161
  value(
166
- value_type(
167
- has_encoding,
168
- encoding_of(:GeneAbundance))))),
162
+ has_encoding,
163
+ encoding_of(G_ENC)))),
169
164
  argument(
170
165
  term(
171
166
  function(
data/lib/bel_parser/language/version2_0/functions/list.rb CHANGED
@@ -14,6 +14,7 @@ module BELParser
14
14
  SHORT = :list
15
15
  LONG = :list
16
16
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::List
17
+ A_ENC = Version2_0::ValueEncodings::Abundance
17
18
  DESCRIPTION = 'Groups a list of terms together.'.freeze
18
19
 
19
20
  def self.short
@@ -51,13 +52,11 @@ module BELParser
51
52
  argument(
52
53
  parameter(
53
54
  prefix(
54
- identifier(
55
- has_namespace,
56
- namespace_of(:*))),
55
+ has_namespace,
56
+ namespace_of(:*)),
57
57
  value(
58
- value_type(
59
- has_encoding,
60
- encoding_of(:Abundance))))))
58
+ has_encoding,
59
+ encoding_of(A_ENC)))))
61
60
  end
62
61
  private_constant :AST
63
62
 
data/lib/bel_parser/language/version2_0/functions/location.rb CHANGED
@@ -14,6 +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
18
  DESCRIPTION = 'Denotes the cellular location of the abundance.'.freeze
18
19
 
19
20
  def self.short
@@ -51,13 +52,11 @@ module BELParser
51
52
  argument(
52
53
  parameter(
53
54
  prefix(
54
- identifier(
55
- has_namespace,
56
- namespace_of(:*))),
55
+ has_namespace,
56
+ namespace_of(:*)),
57
57
  value(
58
- value_type(
59
- has_encoding,
60
- encoding_of(:Location))))))
58
+ has_encoding,
59
+ encoding_of(L_ENC)))))
61
60
  end
62
61
  private_constant :AST
63
62
 
data/lib/bel_parser/language/version2_0/functions/micro_rna_abundance.rb CHANGED
@@ -15,6 +15,7 @@ module BELParser
15
15
  SHORT = :m
16
16
  LONG = :microRNAAbundance
17
17
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::MicroRNAAbundance
18
+ M_ENC = Version2_0::ValueEncodings::MicroRNAAbundance
18
19
  DESCRIPTION = 'Denotes the abundance of a processed, functional
19
20
  icroRNA'.freeze
20
21
 
@@ -53,13 +54,11 @@ module BELParser
53
54
  argument(
54
55
  parameter(
55
56
  prefix(
56
- identifier(
57
- has_namespace,
58
- namespace_of(:*))),
57
+ has_namespace,
58
+ namespace_of(:*)),
59
59
  value(
60
- value_type(
61
- has_encoding,
62
- encoding_of(:MicroRNAAbundance))))))
60
+ has_encoding,
61
+ encoding_of(M_ENC)))))
63
62
  end
64
63
  private_constant :AST
65
64
 
@@ -89,13 +88,11 @@ module BELParser
89
88
  argument(
90
89
  parameter(
91
90
  prefix(
92
- identifier(
93
- has_namespace,
94
- namespace_of(:*))),
91
+ has_namespace,
92
+ namespace_of(:*)),
95
93
  value(
96
- value_type(
97
- has_encoding,
98
- encoding_of(:MicroRNAAbundance))))),
94
+ has_encoding,
95
+ encoding_of(M_ENC)))),
99
96
  argument(
100
97
  term(
101
98
  function(
@@ -130,13 +127,11 @@ module BELParser
130
127
  argument(
131
128
  parameter(
132
129
  prefix(
133
- identifier(
134
- has_namespace,
135
- namespace_of(:*))),
130
+ has_namespace,
131
+ namespace_of(:*)),
136
132
  value(
137
- value_type(
138
- has_encoding,
139
- encoding_of(:MicroRNAAbundance))))),
133
+ has_encoding,
134
+ encoding_of(M_ENC)))),
140
135
  argument(
141
136
  term(
142
137
  function(
data/lib/bel_parser/language/version2_0/functions/molecular_activity.rb CHANGED
@@ -15,6 +15,7 @@ module BELParser
15
15
  SHORT = :ma
16
16
  LONG = :molecularActivity
17
17
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::MolecularActivity
18
+ T_ENC = Version2_0::ValueEncodings::Activity
18
19
  DESCRIPTION = 'Denotes the frequency or abundance of events
19
20
  n which a member acts as a causal agent at the
20
21
  olecular scale'.freeze
@@ -46,7 +47,6 @@ module BELParser
46
47
 
47
48
  private_class_method :new
48
49
 
49
- # TODO: More constraints on prefix for activity namespace?
50
50
  AST = BELParser::Language::Semantics::Builder.build do
51
51
  term(
52
52
  function(
@@ -54,11 +54,12 @@ module BELParser
54
54
  function_of(MolecularActivity))),
55
55
  argument(
56
56
  parameter(
57
- prefix(any),
57
+ prefix(
58
+ has_namespace,
59
+ namespace_of(:*)),
58
60
  value(
59
- value_type(
60
- has_encoding,
61
- encoding_of(:Activity))))))
61
+ has_encoding,
62
+ encoding_of(T_ENC)))))
62
63
  end
63
64
  private_constant :AST
64
65
 
data/lib/bel_parser/language/version2_0/functions/pathology.rb CHANGED
@@ -14,6 +14,7 @@ module BELParser
14
14
  SHORT = :path
15
15
  LONG = :pathology
16
16
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Pathology
17
+ O_ENC = Version2_0::ValueEncodings::Pathology
17
18
  DESCRIPTION = 'Denotes a disease or pathology process'.freeze
18
19
 
19
20
  def self.short
@@ -51,13 +52,11 @@ module BELParser
51
52
  argument(
52
53
  parameter(
53
54
  prefix(
54
- identifier(
55
- has_namespace,
56
- namespace_of(:*))),
55
+ has_namespace,
56
+ namespace_of(:*)),
57
57
  value(
58
- value_type(
59
- has_encoding,
60
- encoding_of(:Pathology))))))
58
+ has_encoding,
59
+ encoding_of(O_ENC)))))
61
60
  end
62
61
  private_constant :AST
63
62
 
data/lib/bel_parser/language/version2_0/functions/protein_abundance.rb CHANGED
@@ -14,6 +14,7 @@ module BELParser
14
14
  SHORT = :p
15
15
  LONG = :proteinAbundance
16
16
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::ProteinAbundance
17
+ P_ENC = Version2_0::ValueEncodings::ProteinAbundance
17
18
  DESCRIPTION = 'Denotes the abundance of a protein'.freeze
18
19
 
19
20
  def self.short
@@ -51,13 +52,11 @@ module BELParser
51
52
  argument(
52
53
  parameter(
53
54
  prefix(
54
- identifier(
55
- has_namespace,
56
- namespace_of(:*))),
55
+ has_namespace,
56
+ namespace_of(:*)),
57
57
  value(
58
- value_type(
59
- has_encoding,
60
- encoding_of(:ProteinAbundance))))))
58
+ has_encoding,
59
+ encoding_of(P_ENC)))))
61
60
  end
62
61
  private_constant :AST
63
62
 
@@ -87,13 +86,11 @@ module BELParser
87
86
  argument(
88
87
  parameter(
89
88
  prefix(
90
- identifier(
91
- has_namespace,
92
- namespace_of(:*))),
89
+ has_namespace,
90
+ namespace_of(:*)),
93
91
  value(
94
- value_type(
95
- has_encoding,
96
- encoding_of(:ProteinAbundance))))),
92
+ has_encoding,
93
+ encoding_of(P_ENC)))),
97
94
  argument(
98
95
  term(
99
96
  function(
@@ -159,13 +156,11 @@ module BELParser
159
156
  argument(
160
157
  parameter(
161
158
  prefix(
162
- identifier(
163
- has_namespace,
164
- namespace_of(:*))),
159
+ has_namespace,
160
+ namespace_of(:*)),
165
161
  value(
166
- value_type(
167
- has_encoding,
168
- encoding_of(:ProteinAbundance))))),
162
+ has_encoding,
163
+ encoding_of(P_ENC)))),
169
164
  argument(
170
165
  term(
171
166
  function(
@@ -200,13 +195,11 @@ module BELParser
200
195
  argument(
201
196
  parameter(
202
197
  prefix(
203
- identifier(
204
- has_namespace,
205
- namespace_of(:*))),
198
+ has_namespace,
199
+ namespace_of(:*)),
206
200
  value(
207
- value_type(
208
- has_encoding,
209
- encoding_of(:ProteinAbundance))))),
201
+ has_encoding,
202
+ encoding_of(P_ENC)))),
210
203
  variadic_arguments(
211
204
  term(
212
205
  function(
@@ -241,13 +234,11 @@ module BELParser
241
234
  argument(
242
235
  parameter(
243
236
  prefix(
244
- identifier(
245
- has_namespace,
246
- namespace_of(:*))),
237
+ has_namespace,
238
+ namespace_of(:*)),
247
239
  value(
248
- value_type(
249
- has_encoding,
250
- encoding_of(:ProteinAbundance))))),
240
+ has_encoding,
241
+ encoding_of(P_ENC)))),
251
242
  argument(
252
243
  term(
253
244
  function(
data/lib/bel_parser/language/version2_0/functions/protein_modification.rb CHANGED
@@ -15,8 +15,8 @@ module BELParser
15
15
 
16
16
  SHORT = :pmod
17
17
  LONG = :proteinModification
18
- RETURN_TYPE =
19
- BELParser::Language::Version2_0::ReturnTypes::ProteinModification
18
+ RETURN_TYPE = Version2_0::ReturnTypes::ProteinModification
19
+ E_ENC = Version2_0::ValueEncodings::ProteinModification
20
20
  DESCRIPTION = 'Denotes a covalently modified protein
21
21
  bundance'.freeze
22
22
 
@@ -57,9 +57,8 @@ module BELParser
57
57
  parameter(
58
58
  prefix(any),
59
59
  value(
60
- value_type(
61
- has_encoding,
62
- encoding_of(:ModificationType))))))
60
+ has_encoding,
61
+ encoding_of(E_ENC)))))
63
62
  end
64
63
  private_constant :AST
65
64
 
@@ -93,15 +92,13 @@ module BELParser
93
92
  parameter(
94
93
  prefix(any),
95
94
  value(
96
- value_type(
97
- has_encoding,
98
- encoding_of(:ModificationType))))),
95
+ has_encoding,
96
+ encoding_of(E_ENC)))),
99
97
  argument(
100
98
  parameter(
101
99
  prefix(any),
102
100
  value(
103
- value_type(
104
- amino_acid_of(*AminoAcid.values))))))
101
+ amino_acid_of(*AminoAcid.values)))))
105
102
  end
106
103
  private_constant :AST
107
104
 
@@ -135,21 +132,18 @@ module BELParser
135
132
  parameter(
136
133
  prefix(any),
137
134
  value(
138
- value_type(
139
- has_encoding,
140
- encoding_of(:ModificationType))))),
135
+ has_encoding,
136
+ encoding_of(E_ENC)))),
141
137
  argument(
142
138
  parameter(
143
139
  prefix(any),
144
140
  value(
145
- value_type(
146
- amino_acid_of(*AminoAcid.values))))),
141
+ amino_acid_of(*AminoAcid.values)))),
147
142
  argument(
148
143
  parameter(
149
144
  prefix(any),
150
145
  value(
151
- value_type(
152
- is_sequence_position)))))
146
+ is_sequence_position))))
153
147
  end
154
148
  private_constant :AST
155
149
 
data/lib/bel_parser/language/version2_0/functions/rna_abundance.rb CHANGED
@@ -14,6 +14,7 @@ module BELParser
14
14
  SHORT = :r
15
15
  LONG = :rnaAbundance
16
16
  RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::GeneAbundance
17
+ R_ENC = Version2_0::ValueEncodings::RNAAbundance
17
18
  DESCRIPTION = 'Denotes the abundance of a gene'.freeze
18
19
 
19
20
  def self.short
@@ -51,13 +52,11 @@ module BELParser
51
52
  argument(
52
53
  parameter(
53
54
  prefix(
54
- identifier(
55
- has_namespace,
56
- namespace_of(:*))),
55
+ has_namespace,
56
+ namespace_of(:*)),
57
57
  value(
58
- value_type(
59
- has_encoding,
60
- encoding_of(:RnaAbundance))))))
58
+ has_encoding,
59
+ encoding_of(R_ENC)))))
61
60
  end
62
61
  private_constant :AST
63
62
 
@@ -118,13 +117,11 @@ module BELParser
118
117
  argument(
119
118
  parameter(
120
119
  prefix(
121
- identifier(
122
- has_namespace,
123
- namespace_of(:*))),
120
+ has_namespace,
121
+ namespace_of(:*)),
124
122
  value(
125
- value_type(
126
- has_encoding,
127
- encoding_of(:RnaAbundance))))),
123
+ has_encoding,
124
+ encoding_of(R_ENC)))),
128
125
  argument(
129
126
  term(
130
127
  function(
@@ -159,13 +156,11 @@ module BELParser
159
156
  argument(
160
157
  parameter(
161
158
  prefix(
162
- identifier(
163
- has_namespace,
164
- namespace_of(:*))),
159
+ has_namespace,
160
+ namespace_of(:*)),
165
161
  value(
166
- value_type(
167
- has_encoding,
168
- encoding_of(:RnaAbundance))))),
162
+ has_encoding,
163
+ encoding_of(R_ENC)))),
169
164
  argument(
170
165
  term(
171
166
  function(
data/lib/bel_parser/language/version2_0/functions/to_location.rb CHANGED
@@ -14,6 +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
18
  DESCRIPTION = 'Denotes the to cellular location of the
18
19
  bundance.'.freeze
19
20
 
@@ -52,13 +53,11 @@ module BELParser
52
53
  argument(
53
54
  parameter(
54
55
  prefix(
55
- identifier(
56
- has_namespace,
57
- namespace_of(:*))),
56
+ has_namespace,
57
+ namespace_of(:*)),
58
58
  value(
59
- value_type(
60
- has_encoding,
61
- encoding_of(:Location))))))
59
+ has_encoding,
60
+ encoding_of(L_ENC)))))
62
61
  end
63
62
  private_constant :AST
64
63
 
data/lib/bel_parser/language/version2_0/functions/variant.rb CHANGED
@@ -53,10 +53,7 @@ module BELParser
53
53
  argument(
54
54
  parameter(
55
55
  prefix(any),
56
- value(
57
- value_type(
58
- has_encoding,
59
- encoding_of(:HgvsVariantDescription))))))
56
+ value(any))))
60
57
  end
61
58
  private_constant :AST
62
59