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/version1_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::Version1_0::ReturnTypes::Fusion
18
+ G_ENC = Version1_0::ValueEncodings::GeneAbundance
19
+ P_ENC = Version1_0::ValueEncodings::ProteinAbundance
20
+ R_ENC = Version1_0::ValueEncodings::RNAAbundance
18
21
  DESCRIPTION = 'Specifies the abundance of a protein translated
19
22
  rom the fusion of a gene'.freeze
20
23
 
@@ -53,27 +56,21 @@ 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),
66
+ prefix(any),
67
67
  value(
68
- value_type(
69
- is_sequence_position)))),
68
+ is_sequence_position))),
70
69
  argument(
71
70
  parameter(
72
- prefix(
73
- any),
71
+ prefix(any),
74
72
  value(
75
- value_type(
76
- is_sequence_position)))))
73
+ is_sequence_position))))
77
74
  end
78
75
  private_constant :AST
79
76
 
@@ -103,13 +100,11 @@ module BELParser
103
100
  argument(
104
101
  parameter(
105
102
  prefix(
106
- identifier(
107
- has_namespace,
108
- namespace_of(:*))),
103
+ has_namespace,
104
+ namespace_of(:*)),
109
105
  value(
110
- value_type(
111
- has_encoding,
112
- encoding_of(:GeneAbundance))))))
106
+ has_encoding,
107
+ encoding_of(G_ENC)))))
113
108
  end
114
109
  private_constant :AST
115
110
 
@@ -139,27 +134,21 @@ module BELParser
139
134
  argument(
140
135
  parameter(
141
136
  prefix(
142
- identifier(
143
- has_namespace,
144
- namespace_of(:*))),
137
+ has_namespace,
138
+ namespace_of(:*)),
145
139
  value(
146
- value_type(
147
- has_encoding,
148
- encoding_of(:ProteinAbundance))))),
140
+ has_encoding,
141
+ encoding_of(P_ENC)))),
149
142
  argument(
150
143
  parameter(
151
- prefix(
152
- any),
144
+ prefix(any),
153
145
  value(
154
- value_type(
155
- is_sequence_position)))),
146
+ is_sequence_position))),
156
147
  argument(
157
148
  parameter(
158
- prefix(
159
- any),
149
+ prefix(any),
160
150
  value(
161
- value_type(
162
- is_sequence_position)))))
151
+ is_sequence_position))))
163
152
  end
164
153
  private_constant :AST
165
154
 
@@ -189,13 +178,11 @@ module BELParser
189
178
  argument(
190
179
  parameter(
191
180
  prefix(
192
- identifier(
193
- has_namespace,
194
- namespace_of(:*))),
181
+ has_namespace,
182
+ namespace_of(:*)),
195
183
  value(
196
- value_type(
197
- has_encoding,
198
- encoding_of(:ProteinAbundance))))))
184
+ has_encoding,
185
+ encoding_of(P_ENC)))))
199
186
  end
200
187
  private_constant :AST
201
188
 
@@ -225,27 +212,21 @@ module BELParser
225
212
  argument(
226
213
  parameter(
227
214
  prefix(
228
- identifier(
229
- has_namespace,
230
- namespace_of(:*))),
215
+ has_namespace,
216
+ namespace_of(:*)),
231
217
  value(
232
- value_type(
233
- has_encoding,
234
- encoding_of(:RnaAbundance))))),
218
+ has_encoding,
219
+ encoding_of(R_ENC)))),
235
220
  argument(
236
221
  parameter(
237
- prefix(
238
- any),
222
+ prefix(any),
239
223
  value(
240
- value_type(
241
- is_sequence_position)))),
224
+ is_sequence_position))),
242
225
  argument(
243
226
  parameter(
244
- prefix(
245
- any),
227
+ prefix(any),
246
228
  value(
247
- value_type(
248
- is_sequence_position)))))
229
+ is_sequence_position))))
249
230
  end
250
231
  private_constant :AST
251
232
 
@@ -275,13 +256,11 @@ module BELParser
275
256
  argument(
276
257
  parameter(
277
258
  prefix(
278
- identifier(
279
- has_namespace,
280
- namespace_of(:*))),
259
+ has_namespace,
260
+ namespace_of(:*)),
281
261
  value(
282
- value_type(
283
- has_encoding,
284
- encoding_of(:RnaAbundance))))))
262
+ has_encoding,
263
+ encoding_of(R_ENC)))))
285
264
  end
286
265
  private_constant :AST
287
266
 
data/lib/bel_parser/language/version1_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::Version1_0::ReturnTypes::GeneAbundance
17
+ G_ENC = Version1_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
  argument(
62
61
  term(
63
62
  function(
@@ -92,13 +91,11 @@ module BELParser
92
91
  argument(
93
92
  parameter(
94
93
  prefix(
95
- identifier(
96
- has_namespace,
97
- namespace_of(:*))),
94
+ has_namespace,
95
+ namespace_of(:*)),
98
96
  value(
99
- value_type(
100
- has_encoding,
101
- encoding_of(:GeneAbundance))))))
97
+ has_encoding,
98
+ encoding_of(G_ENC)))))
102
99
  end
103
100
  private_constant :AST
104
101
 
data/lib/bel_parser/language/version1_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::Version1_0::ReturnTypes::List
17
+ A_ENC = Version1_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/version1_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::Version1_0::ReturnTypes::MicroRNAAbundance
18
+ M_ENC = Version1_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
 
data/lib/bel_parser/language/version1_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::Version1_0::ReturnTypes::Pathology
17
+ O_ENC = Version1_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/version1_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::Version1_0::ReturnTypes::ProteinAbundance
17
+ PROTEIN_ENC = BELParser::Language::Version1_0::ValueEncodings::ProteinAbundance
17
18
  DESCRIPTION = 'Denotes the abundance of a protein'.freeze
18
19
 
19
20
  def self.short
@@ -51,13 +52,10 @@ module BELParser
51
52
  argument(
52
53
  parameter(
53
54
  prefix(
54
- identifier(
55
- has_namespace,
56
- namespace_of(:*))),
55
+ has_namespace),
57
56
  value(
58
- value_type(
59
- has_encoding,
60
- encoding_of(:ProteinAbundance))))),
57
+ has_encoding,
58
+ encoding_of(PROTEIN_ENC)))),
61
59
  argument(
62
60
  term(
63
61
  function(
@@ -92,13 +90,10 @@ module BELParser
92
90
  argument(
93
91
  parameter(
94
92
  prefix(
95
- identifier(
96
- has_namespace,
97
- namespace_of(:*))),
93
+ has_namespace),
98
94
  value(
99
- value_type(
100
- has_encoding,
101
- encoding_of(:ProteinAbundance))))),
95
+ has_encoding,
96
+ encoding_of(PROTEIN_ENC)))),
102
97
  argument(
103
98
  term(
104
99
  function(
@@ -133,13 +128,10 @@ module BELParser
133
128
  argument(
134
129
  parameter(
135
130
  prefix(
136
- identifier(
137
- has_namespace,
138
- namespace_of(:*))),
131
+ has_namespace),
139
132
  value(
140
- value_type(
141
- has_encoding,
142
- encoding_of(:ProteinAbundance))))),
133
+ has_encoding,
134
+ encoding_of(PROTEIN_ENC)))),
143
135
  argument(
144
136
  term(
145
137
  function(
@@ -174,13 +166,10 @@ module BELParser
174
166
  argument(
175
167
  parameter(
176
168
  prefix(
177
- identifier(
178
- has_namespace,
179
- namespace_of(:*))),
169
+ has_namespace),
180
170
  value(
181
- value_type(
182
- has_encoding,
183
- encoding_of(:ProteinAbundance))))),
171
+ has_encoding,
172
+ encoding_of(PROTEIN_ENC)))),
184
173
  argument(
185
174
  term(
186
175
  function(
@@ -215,13 +204,10 @@ module BELParser
215
204
  argument(
216
205
  parameter(
217
206
  prefix(
218
- identifier(
219
- has_namespace,
220
- namespace_of(:*))),
207
+ has_namespace),
221
208
  value(
222
- value_type(
223
- has_encoding,
224
- encoding_of(:ProteinAbundance))))))
209
+ has_encoding,
210
+ encoding_of(PROTEIN_ENC)))))
225
211
  end
226
212
  private_constant :AST
227
213
 
data/lib/bel_parser/language/version1_0/functions/protein_modification.rb CHANGED
@@ -55,26 +55,20 @@ module BELParser
55
55
  function_of(ProteinModification))),
56
56
  argument(
57
57
  parameter(
58
- prefix(
59
- any),
58
+ prefix(any),
60
59
  value(
61
- value_type(
62
- covalent_protein_modification_of(
63
- *CovalentProteinModification.values))))),
60
+ covalent_protein_modification_of(
61
+ *CovalentProteinModification.values)))),
64
62
  argument(
65
63
  parameter(
66
- prefix(
67
- any),
64
+ prefix(any),
68
65
  value(
69
- value_type(
70
- amino_acid_of(*AminoAcid.values))))),
66
+ amino_acid_of(*AminoAcid.values)))),
71
67
  argument(
72
68
  parameter(
73
- prefix(
74
- any),
69
+ prefix(any),
75
70
  value(
76
- value_type(
77
- is_sequence_position)))))
71
+ is_sequence_position))))
78
72
  end
79
73
  private_constant :AST
80
74
 
@@ -109,19 +103,15 @@ module BELParser
109
103
  function_of(ProteinModification))),
110
104
  argument(
111
105
  parameter(
112
- prefix(
113
- any),
106
+ prefix(any),
114
107
  value(
115
- value_type(
116
- covalent_protein_modification_of(
117
- *CovalentProteinModification.values))))),
108
+ covalent_protein_modification_of(
109
+ *CovalentProteinModification.values)))),
118
110
  argument(
119
111
  parameter(
120
- prefix(
121
- any),
112
+ prefix(any),
122
113
  value(
123
- value_type(
124
- amino_acid_of(*AminoAcid.values))))))
114
+ amino_acid_of(*AminoAcid.values)))))
125
115
  end
126
116
  private_constant :AST
127
117
 
@@ -155,12 +145,10 @@ module BELParser
155
145
  function_of(ProteinModification))),
156
146
  argument(
157
147
  parameter(
158
- prefix(
159
- any),
148
+ prefix(any),
160
149
  value(
161
- value_type(
162
- covalent_protein_modification_of(
163
- *CovalentProteinModification.values))))))
150
+ covalent_protein_modification_of(
151
+ *CovalentProteinModification.values)))))
164
152
  end
165
153
  private_constant :AST
166
154
 
data/lib/bel_parser/language/version1_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::Version1_0::ReturnTypes::GeneAbundance
17
+ R_ENC = Version1_0::ReturnTypes::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
58
  has_encoding,
60
- encoding_of(:RnaAbundance))))),
59
+ encoding_of(R_ENC)))),
61
60
  argument(
62
61
  term(
63
62
  function(
@@ -92,13 +91,11 @@ module BELParser
92
91
  argument(
93
92
  parameter(
94
93
  prefix(
95
- identifier(
96
- has_namespace,
97
- namespace_of(:*))),
94
+ has_namespace,
95
+ namespace_of(:*)),
98
96
  value(
99
- value_type(
100
- has_encoding,
101
- encoding_of(:RnaAbundance))))))
97
+ has_encoding,
98
+ encoding_of(R_ENC)))))
102
99
  end
103
100
  private_constant :AST
104
101
 
data/lib/bel_parser/language/version1_0/functions/substitution.rb CHANGED
@@ -52,25 +52,19 @@ module BELParser
52
52
  function_of(Substitution))),
53
53
  argument(
54
54
  parameter(
55
- prefix(
56
- any),
55
+ prefix(any),
57
56
  value(
58
- value_type(
59
- amino_acid_of(*AminoAcid.values))))),
57
+ amino_acid_of(*AminoAcid.values)))),
60
58
  argument(
61
59
  parameter(
62
- prefix(
63
- any),
60
+ prefix(any),
64
61
  value(
65
- value_type(
66
- is_sequence_position)))),
62
+ is_sequence_position))),
67
63
  argument(
68
64
  parameter(
69
- prefix(
70
- any),
65
+ prefix(any),
71
66
  value(
72
- value_type(
73
- amino_acid_of(*AminoAcid.values))))))
67
+ amino_acid_of(*AminoAcid.values)))))
74
68
  end
75
69
  private_constant :AST
76
70
 
data/lib/bel_parser/language/version1_0/functions/translocation.rb CHANGED
@@ -15,6 +15,7 @@ module BELParser
15
15
  SHORT = :tloc
16
16
  LONG = :translocation
17
17
  RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Abundance
18
+ A_ENC = Version1_0::ValueEncodings::Abundance
18
19
  DESCRIPTION = 'Denotes the frequency or abundance of events
19
20
  n which members move between locations'.freeze
20
21
 
@@ -58,23 +59,19 @@ module BELParser
58
59
  argument(
59
60
  parameter(
60
61
  prefix(
61
- identifier(
62
- has_namespace,
63
- namespace_of(:*))),
62
+ has_namespace,
63
+ namespace_of(:*)),
64
64
  value(
65
- value_type(
66
- has_encoding,
67
- encoding_of(:Abundance))))),
65
+ has_encoding,
66
+ encoding_of(A_ENC)))),
68
67
  argument(
69
68
  parameter(
70
69
  prefix(
71
- identifier(
72
- has_namespace,
73
- namespace_of(:*))),
70
+ has_namespace,
71
+ namespace_of(:*)),
74
72
  value(
75
- value_type(
76
- has_encoding,
77
- encoding_of(:Abundance))))))
73
+ has_encoding,
74
+ encoding_of(A_ENC)))))
78
75
  end
79
76
  private_constant :AST
80
77
 
data/lib/bel_parser/language/version1_0/functions/truncation.rb CHANGED
@@ -52,11 +52,9 @@ module BELParser
52
52
  function_of(Truncation))),
53
53
  argument(
54
54
  parameter(
55
- prefix(
56
- any),
55
+ prefix(any),
57
56
  value(
58
- value_type(
59
- is_sequence_position)))))
57
+ is_sequence_position))))
60
58
  end
61
59
  private_constant :AST
62
60
 
data/lib/bel_parser/language/version1_0/value_encodings/abundance.rb ADDED
@@ -0,0 +1,21 @@
1
+ require_relative '../../version1_0'
2
+ require_relative 'any'
3
+
4
+ module BELParser
5
+ module Language
6
+ module Version1_0
7
+ module ValueEncodings
8
+ # Abundance value encoding.
9
+ class Abundance < Any
10
+ # Return the {Symbol} value.
11
+ #
12
+ # @note This method should be overridden in subclasses.
13
+ def self.to_sym
14
+ raise_not_implemented(__method__) if self != Abundance
15
+ :A
16
+ end
17
+ end
18
+ end
19
+ end
20
+ end
21
+ end