bel_parser 1.0.0.alpha.27-java
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- checksums.yaml +7 -0
- data/.gemspec-java +32 -0
- data/CHANGELOG.md +10 -0
- data/LICENSE +191 -0
- data/README.md +20 -0
- data/VERSION +1 -0
- data/bin/bel2_validator +62 -0
- data/bin/bel_script_reader +132 -0
- data/lib/bel/translator/plugins/bel_script.rb +38 -0
- data/lib/bel/translator/plugins/bel_script/bel_citation_serialization.rb +125 -0
- data/lib/bel/translator/plugins/bel_script/bel_discrete_serialization.rb +109 -0
- data/lib/bel/translator/plugins/bel_script/bel_top_down_serialization.rb +100 -0
- data/lib/bel/translator/plugins/bel_script/nanopub_serialization.rb +79 -0
- data/lib/bel/translator/plugins/bel_script/reader.rb +39 -0
- data/lib/bel/translator/plugins/bel_script/translator.rb +37 -0
- data/lib/bel/translator/plugins/bel_script/writer.rb +180 -0
- data/lib/bel_parser.rb +23 -0
- data/lib/bel_parser/ast_filter.rb +44 -0
- data/lib/bel_parser/ast_generator.rb +83 -0
- data/lib/bel_parser/expression.rb +3 -0
- data/lib/bel_parser/expression/filter.rb +31 -0
- data/lib/bel_parser/expression/parser.rb +72 -0
- data/lib/bel_parser/expression/validator.rb +79 -0
- data/lib/bel_parser/language.rb +114 -0
- data/lib/bel_parser/language/amino_acid.rb +68 -0
- data/lib/bel_parser/language/apply_namespace_encoding.rb +98 -0
- data/lib/bel_parser/language/base_specification.rb +82 -0
- data/lib/bel_parser/language/covalent_protein_modification.rb +56 -0
- data/lib/bel_parser/language/expression_validator.rb +68 -0
- data/lib/bel_parser/language/function.rb +67 -0
- data/lib/bel_parser/language/relationship.rb +102 -0
- data/lib/bel_parser/language/semantics.rb +40 -0
- data/lib/bel_parser/language/semantics/deeply_nested_statement.rb +65 -0
- data/lib/bel_parser/language/semantics/function_deprecation.rb +43 -0
- data/lib/bel_parser/language/semantics/list_function_subject.rb +45 -0
- data/lib/bel_parser/language/semantics/multiple_subject_object.rb +55 -0
- data/lib/bel_parser/language/semantics/non_causal_nested_statement.rb +50 -0
- data/lib/bel_parser/language/semantics/non_object_list.rb +56 -0
- data/lib/bel_parser/language/semantics/relationship_deprecation.rb +44 -0
- data/lib/bel_parser/language/semantics/relationship_not_listable.rb +60 -0
- data/lib/bel_parser/language/semantics/signature_mapping.rb +83 -0
- data/lib/bel_parser/language/semantics_ast.rb +784 -0
- data/lib/bel_parser/language/semantics_ast_warnings.rb +180 -0
- data/lib/bel_parser/language/semantics_function.rb +16 -0
- data/lib/bel_parser/language/semantics_match.rb +28 -0
- data/lib/bel_parser/language/semantics_result.rb +33 -0
- data/lib/bel_parser/language/semantics_type_warning.rb +22 -0
- data/lib/bel_parser/language/semantics_warning.rb +27 -0
- data/lib/bel_parser/language/signature.rb +39 -0
- data/lib/bel_parser/language/specification.rb +118 -0
- data/lib/bel_parser/language/syntax.rb +38 -0
- data/lib/bel_parser/language/syntax/invalid_function.rb +39 -0
- data/lib/bel_parser/language/syntax/invalid_relationship.rb +42 -0
- data/lib/bel_parser/language/syntax/undefined_namespace.rb +49 -0
- data/lib/bel_parser/language/syntax/undefined_namespace_value.rb +44 -0
- data/lib/bel_parser/language/syntax_error.rb +32 -0
- data/lib/bel_parser/language/syntax_function.rb +16 -0
- data/lib/bel_parser/language/syntax_result.rb +32 -0
- data/lib/bel_parser/language/syntax_warning.rb +27 -0
- data/lib/bel_parser/language/version1_0.rb +20 -0
- data/lib/bel_parser/language/version1_0/functions/abundance.rb +83 -0
- data/lib/bel_parser/language/version1_0/functions/biological_process.rb +83 -0
- data/lib/bel_parser/language/version1_0/functions/catalytic_activity.rb +114 -0
- data/lib/bel_parser/language/version1_0/functions/cell_secretion.rb +83 -0
- data/lib/bel_parser/language/version1_0/functions/cell_surface_expression.rb +83 -0
- data/lib/bel_parser/language/version1_0/functions/chaperone_activity.rb +114 -0
- data/lib/bel_parser/language/version1_0/functions/complex_abundance.rb +115 -0
- data/lib/bel_parser/language/version1_0/functions/composite_abundance.rb +81 -0
- data/lib/bel_parser/language/version1_0/functions/degradation.rb +83 -0
- data/lib/bel_parser/language/version1_0/functions/fusion.rb +287 -0
- data/lib/bel_parser/language/version1_0/functions/gene_abundance.rb +122 -0
- data/lib/bel_parser/language/version1_0/functions/gtp_bound_activity.rb +113 -0
- data/lib/bel_parser/language/version1_0/functions/kinase_activity.rb +114 -0
- data/lib/bel_parser/language/version1_0/functions/list.rb +114 -0
- data/lib/bel_parser/language/version1_0/functions/micro_rna_abundance.rb +85 -0
- data/lib/bel_parser/language/version1_0/functions/molecular_activity.rb +82 -0
- data/lib/bel_parser/language/version1_0/functions/pathology.rb +83 -0
- data/lib/bel_parser/language/version1_0/functions/peptidase_activity.rb +112 -0
- data/lib/bel_parser/language/version1_0/functions/phosphatase_activity.rb +112 -0
- data/lib/bel_parser/language/version1_0/functions/products.rb +79 -0
- data/lib/bel_parser/language/version1_0/functions/protein_abundance.rb +234 -0
- data/lib/bel_parser/language/version1_0/functions/protein_modification.rb +179 -0
- data/lib/bel_parser/language/version1_0/functions/reactants.rb +79 -0
- data/lib/bel_parser/language/version1_0/functions/reaction.rb +86 -0
- data/lib/bel_parser/language/version1_0/functions/ribosylation_activity.rb +114 -0
- data/lib/bel_parser/language/version1_0/functions/rna_abundance.rb +122 -0
- data/lib/bel_parser/language/version1_0/functions/substitution.rb +93 -0
- data/lib/bel_parser/language/version1_0/functions/transcriptional_activity.rb +114 -0
- data/lib/bel_parser/language/version1_0/functions/translocation.rb +98 -0
- data/lib/bel_parser/language/version1_0/functions/transport_activity.rb +115 -0
- data/lib/bel_parser/language/version1_0/functions/truncation.rb +81 -0
- data/lib/bel_parser/language/version1_0/relationships/acts_in.rb +61 -0
- data/lib/bel_parser/language/version1_0/relationships/analogous.rb +41 -0
- data/lib/bel_parser/language/version1_0/relationships/association.rb +42 -0
- data/lib/bel_parser/language/version1_0/relationships/biomarker_for.rb +42 -0
- data/lib/bel_parser/language/version1_0/relationships/causes_no_change.rb +50 -0
- data/lib/bel_parser/language/version1_0/relationships/decreases.rb +63 -0
- data/lib/bel_parser/language/version1_0/relationships/directly_decreases.rb +56 -0
- data/lib/bel_parser/language/version1_0/relationships/directly_increases.rb +56 -0
- data/lib/bel_parser/language/version1_0/relationships/has_component.rb +62 -0
- data/lib/bel_parser/language/version1_0/relationships/has_components.rb +61 -0
- data/lib/bel_parser/language/version1_0/relationships/has_member.rb +48 -0
- data/lib/bel_parser/language/version1_0/relationships/has_members.rb +57 -0
- data/lib/bel_parser/language/version1_0/relationships/has_modification.rb +54 -0
- data/lib/bel_parser/language/version1_0/relationships/has_product.rb +60 -0
- data/lib/bel_parser/language/version1_0/relationships/has_variant.rb +54 -0
- data/lib/bel_parser/language/version1_0/relationships/includes.rb +59 -0
- data/lib/bel_parser/language/version1_0/relationships/increases.rb +63 -0
- data/lib/bel_parser/language/version1_0/relationships/is_a.rb +48 -0
- data/lib/bel_parser/language/version1_0/relationships/negative_correlation.rb +50 -0
- data/lib/bel_parser/language/version1_0/relationships/orthologous.rb +48 -0
- data/lib/bel_parser/language/version1_0/relationships/positive_correlation.rb +46 -0
- data/lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb +44 -0
- data/lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb +53 -0
- data/lib/bel_parser/language/version1_0/relationships/reactant_in.rb +60 -0
- data/lib/bel_parser/language/version1_0/relationships/sub_process_of.rb +55 -0
- data/lib/bel_parser/language/version1_0/relationships/transcribed_to.rb +53 -0
- data/lib/bel_parser/language/version1_0/relationships/translated_to.rb +54 -0
- data/lib/bel_parser/language/version1_0/relationships/translocates.rb +57 -0
- data/lib/bel_parser/language/version1_0/return_types/abundance.rb +20 -0
- data/lib/bel_parser/language/version1_0/return_types/any.rb +74 -0
- data/lib/bel_parser/language/version1_0/return_types/biological_process.rb +17 -0
- data/lib/bel_parser/language/version1_0/return_types/catalytic_activity.rb +20 -0
- data/lib/bel_parser/language/version1_0/return_types/chaperone_activity.rb +20 -0
- data/lib/bel_parser/language/version1_0/return_types/complex_abundance.rb +17 -0
- data/lib/bel_parser/language/version1_0/return_types/fusion.rb +17 -0
- data/lib/bel_parser/language/version1_0/return_types/gene_abundance.rb +17 -0
- data/lib/bel_parser/language/version1_0/return_types/gtp_bound_activity.rb +20 -0
- data/lib/bel_parser/language/version1_0/return_types/kinase_activity.rb +20 -0
- data/lib/bel_parser/language/version1_0/return_types/list.rb +17 -0
- data/lib/bel_parser/language/version1_0/return_types/micro_rna_abundance.rb +17 -0
- data/lib/bel_parser/language/version1_0/return_types/molecular_activity.rb +20 -0
- data/lib/bel_parser/language/version1_0/return_types/pathology.rb +17 -0
- data/lib/bel_parser/language/version1_0/return_types/peptidase_activity.rb +20 -0
- data/lib/bel_parser/language/version1_0/return_types/phosphatase_activity.rb +20 -0
- data/lib/bel_parser/language/version1_0/return_types/products.rb +17 -0
- data/lib/bel_parser/language/version1_0/return_types/protein_abundance.rb +17 -0
- data/lib/bel_parser/language/version1_0/return_types/protein_modification.rb +17 -0
- data/lib/bel_parser/language/version1_0/return_types/reactants.rb +17 -0
- data/lib/bel_parser/language/version1_0/return_types/ribosylation_activity.rb +20 -0
- data/lib/bel_parser/language/version1_0/return_types/rna_abundance.rb +17 -0
- data/lib/bel_parser/language/version1_0/return_types/substitution.rb +17 -0
- data/lib/bel_parser/language/version1_0/return_types/transcriptional_activity.rb +20 -0
- data/lib/bel_parser/language/version1_0/return_types/transport_activity.rb +20 -0
- data/lib/bel_parser/language/version1_0/return_types/truncation.rb +17 -0
- data/lib/bel_parser/language/version1_0/value_encodings/abundance.rb +21 -0
- data/lib/bel_parser/language/version1_0/value_encodings/any.rb +74 -0
- data/lib/bel_parser/language/version1_0/value_encodings/biological_process.rb +21 -0
- data/lib/bel_parser/language/version1_0/value_encodings/complex_abundance.rb +21 -0
- data/lib/bel_parser/language/version1_0/value_encodings/gene_abundance.rb +21 -0
- data/lib/bel_parser/language/version1_0/value_encodings/micro_rna_abundance.rb +21 -0
- data/lib/bel_parser/language/version1_0/value_encodings/pathology.rb +21 -0
- data/lib/bel_parser/language/version1_0/value_encodings/protein_abundance.rb +21 -0
- data/lib/bel_parser/language/version1_0/value_encodings/rna_abundance.rb +21 -0
- data/lib/bel_parser/language/version2_0.rb +20 -0
- data/lib/bel_parser/language/version2_0/functions/abundance.rb +161 -0
- data/lib/bel_parser/language/version2_0/functions/activity.rb +118 -0
- data/lib/bel_parser/language/version2_0/functions/biological_process.rb +84 -0
- data/lib/bel_parser/language/version2_0/functions/cell_secretion.rb +83 -0
- data/lib/bel_parser/language/version2_0/functions/cell_surface_expression.rb +83 -0
- data/lib/bel_parser/language/version2_0/functions/complex_abundance.rb +190 -0
- data/lib/bel_parser/language/version2_0/functions/composite_abundance.rb +81 -0
- data/lib/bel_parser/language/version2_0/functions/degradation.rb +83 -0
- data/lib/bel_parser/language/version2_0/functions/fragment.rb +116 -0
- data/lib/bel_parser/language/version2_0/functions/from_location.rb +85 -0
- data/lib/bel_parser/language/version2_0/functions/fusion.rb +203 -0
- data/lib/bel_parser/language/version2_0/functions/gene_abundance.rb +192 -0
- data/lib/bel_parser/language/version2_0/functions/list.rb +114 -0
- data/lib/bel_parser/language/version2_0/functions/location.rb +83 -0
- data/lib/bel_parser/language/version2_0/functions/micro_rna_abundance.rb +163 -0
- data/lib/bel_parser/language/version2_0/functions/molecular_activity.rb +86 -0
- data/lib/bel_parser/language/version2_0/functions/pathology.rb +83 -0
- data/lib/bel_parser/language/version2_0/functions/products.rb +79 -0
- data/lib/bel_parser/language/version2_0/functions/protein_abundance.rb +270 -0
- data/lib/bel_parser/language/version2_0/functions/protein_modification.rb +172 -0
- data/lib/bel_parser/language/version2_0/functions/reactants.rb +79 -0
- data/lib/bel_parser/language/version2_0/functions/reaction.rb +86 -0
- data/lib/bel_parser/language/version2_0/functions/rna_abundance.rb +192 -0
- data/lib/bel_parser/language/version2_0/functions/to_location.rb +84 -0
- data/lib/bel_parser/language/version2_0/functions/translocation.rb +91 -0
- data/lib/bel_parser/language/version2_0/functions/variant.rb +80 -0
- data/lib/bel_parser/language/version2_0/relationships/acts_in.rb +61 -0
- data/lib/bel_parser/language/version2_0/relationships/analogous.rb +45 -0
- data/lib/bel_parser/language/version2_0/relationships/association.rb +42 -0
- data/lib/bel_parser/language/version2_0/relationships/biomarker_for.rb +46 -0
- data/lib/bel_parser/language/version2_0/relationships/causes_no_change.rb +50 -0
- data/lib/bel_parser/language/version2_0/relationships/decreases.rb +63 -0
- data/lib/bel_parser/language/version2_0/relationships/directly_decreases.rb +56 -0
- data/lib/bel_parser/language/version2_0/relationships/directly_increases.rb +56 -0
- data/lib/bel_parser/language/version2_0/relationships/has_component.rb +62 -0
- data/lib/bel_parser/language/version2_0/relationships/has_components.rb +61 -0
- data/lib/bel_parser/language/version2_0/relationships/has_member.rb +48 -0
- data/lib/bel_parser/language/version2_0/relationships/has_members.rb +57 -0
- data/lib/bel_parser/language/version2_0/relationships/has_modification.rb +54 -0
- data/lib/bel_parser/language/version2_0/relationships/has_product.rb +60 -0
- data/lib/bel_parser/language/version2_0/relationships/has_variant.rb +54 -0
- data/lib/bel_parser/language/version2_0/relationships/includes.rb +59 -0
- data/lib/bel_parser/language/version2_0/relationships/increases.rb +63 -0
- data/lib/bel_parser/language/version2_0/relationships/is_a.rb +48 -0
- data/lib/bel_parser/language/version2_0/relationships/negative_correlation.rb +50 -0
- data/lib/bel_parser/language/version2_0/relationships/orthologous.rb +48 -0
- data/lib/bel_parser/language/version2_0/relationships/positive_correlation.rb +46 -0
- data/lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb +48 -0
- data/lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb +53 -0
- data/lib/bel_parser/language/version2_0/relationships/reactant_in.rb +60 -0
- data/lib/bel_parser/language/version2_0/relationships/regulates.rb +51 -0
- data/lib/bel_parser/language/version2_0/relationships/sub_process_of.rb +55 -0
- data/lib/bel_parser/language/version2_0/relationships/transcribed_to.rb +53 -0
- data/lib/bel_parser/language/version2_0/relationships/translated_to.rb +54 -0
- data/lib/bel_parser/language/version2_0/relationships/translocates.rb +57 -0
- data/lib/bel_parser/language/version2_0/return_types/abundance.rb +20 -0
- data/lib/bel_parser/language/version2_0/return_types/activity.rb +20 -0
- data/lib/bel_parser/language/version2_0/return_types/any.rb +74 -0
- data/lib/bel_parser/language/version2_0/return_types/biological_process.rb +17 -0
- data/lib/bel_parser/language/version2_0/return_types/complex_abundance.rb +17 -0
- data/lib/bel_parser/language/version2_0/return_types/fragment.rb +20 -0
- data/lib/bel_parser/language/version2_0/return_types/from_location.rb +20 -0
- data/lib/bel_parser/language/version2_0/return_types/fusion.rb +17 -0
- data/lib/bel_parser/language/version2_0/return_types/gene_abundance.rb +17 -0
- data/lib/bel_parser/language/version2_0/return_types/list.rb +17 -0
- data/lib/bel_parser/language/version2_0/return_types/location.rb +20 -0
- data/lib/bel_parser/language/version2_0/return_types/micro_rna_abundance.rb +17 -0
- data/lib/bel_parser/language/version2_0/return_types/molecular_activity.rb +20 -0
- data/lib/bel_parser/language/version2_0/return_types/pathology.rb +17 -0
- data/lib/bel_parser/language/version2_0/return_types/products.rb +17 -0
- data/lib/bel_parser/language/version2_0/return_types/protein_abundance.rb +17 -0
- data/lib/bel_parser/language/version2_0/return_types/protein_modification.rb +17 -0
- data/lib/bel_parser/language/version2_0/return_types/reactants.rb +17 -0
- data/lib/bel_parser/language/version2_0/return_types/rna_abundance.rb +17 -0
- data/lib/bel_parser/language/version2_0/return_types/to_location.rb +20 -0
- data/lib/bel_parser/language/version2_0/return_types/variant.rb +20 -0
- data/lib/bel_parser/language/version2_0/value_encodings/abundance.rb +21 -0
- data/lib/bel_parser/language/version2_0/value_encodings/activity.rb +21 -0
- data/lib/bel_parser/language/version2_0/value_encodings/any.rb +74 -0
- data/lib/bel_parser/language/version2_0/value_encodings/biological_process.rb +21 -0
- data/lib/bel_parser/language/version2_0/value_encodings/complex_abundance.rb +21 -0
- data/lib/bel_parser/language/version2_0/value_encodings/gene_abundance.rb +21 -0
- data/lib/bel_parser/language/version2_0/value_encodings/location.rb +21 -0
- data/lib/bel_parser/language/version2_0/value_encodings/micro_rna_abundance.rb +21 -0
- data/lib/bel_parser/language/version2_0/value_encodings/pathology.rb +21 -0
- data/lib/bel_parser/language/version2_0/value_encodings/protein_abundance.rb +21 -0
- data/lib/bel_parser/language/version2_0/value_encodings/protein_modification.rb +21 -0
- data/lib/bel_parser/language/version2_0/value_encodings/rna_abundance.rb +21 -0
- data/lib/bel_parser/mixin/line_continuator.rb +15 -0
- data/lib/bel_parser/mixin/line_mapping.rb +14 -0
- data/lib/bel_parser/parsers/ast/node.rb +987 -0
- data/lib/bel_parser/parsers/ast/sexp.rb +8 -0
- data/lib/bel_parser/parsers/bel_script.rb +5 -0
- data/lib/bel_parser/parsers/bel_script/define_annotation.rb +5920 -0
- data/lib/bel_parser/parsers/bel_script/define_annotation.rl +141 -0
- data/lib/bel_parser/parsers/bel_script/define_namespace.rb +1780 -0
- data/lib/bel_parser/parsers/bel_script/define_namespace.rl +121 -0
- data/lib/bel_parser/parsers/bel_script/set.rb +5008 -0
- data/lib/bel_parser/parsers/bel_script/set.rl +116 -0
- data/lib/bel_parser/parsers/bel_script/set_document.rb +7722 -0
- data/lib/bel_parser/parsers/bel_script/set_document.rl +97 -0
- data/lib/bel_parser/parsers/bel_script/unset.rb +706 -0
- data/lib/bel_parser/parsers/bel_script/unset.rl +95 -0
- data/lib/bel_parser/parsers/common.rb +5 -0
- data/lib/bel_parser/parsers/common/blank_line.rb +211 -0
- data/lib/bel_parser/parsers/common/blank_line.rl +81 -0
- data/lib/bel_parser/parsers/common/comment_line.rb +245 -0
- data/lib/bel_parser/parsers/common/comment_line.rl +97 -0
- data/lib/bel_parser/parsers/common/common.rb +7 -0
- data/lib/bel_parser/parsers/common/common.rl +13 -0
- data/lib/bel_parser/parsers/common/identifier.rb +289 -0
- data/lib/bel_parser/parsers/common/identifier.rl +106 -0
- data/lib/bel_parser/parsers/common/list.rb +2388 -0
- data/lib/bel_parser/parsers/common/list.rl +146 -0
- data/lib/bel_parser/parsers/common/string.rb +271 -0
- data/lib/bel_parser/parsers/common/string.rl +107 -0
- data/lib/bel_parser/parsers/expression.rb +7 -0
- data/lib/bel_parser/parsers/expression/comment.rb +239 -0
- data/lib/bel_parser/parsers/expression/comment.rl +97 -0
- data/lib/bel_parser/parsers/expression/nested_statement.rb +17802 -0
- data/lib/bel_parser/parsers/expression/nested_statement.rl +141 -0
- data/lib/bel_parser/parsers/expression/observed_term.rb +7291 -0
- data/lib/bel_parser/parsers/expression/observed_term.rl +92 -0
- data/lib/bel_parser/parsers/expression/parameter.rb +1506 -0
- data/lib/bel_parser/parsers/expression/parameter.rl +97 -0
- data/lib/bel_parser/parsers/expression/relationship.rb +254 -0
- data/lib/bel_parser/parsers/expression/relationship.rl +98 -0
- data/lib/bel_parser/parsers/expression/simple_statement.rb +10475 -0
- data/lib/bel_parser/parsers/expression/simple_statement.rl +112 -0
- data/lib/bel_parser/parsers/expression/term.rb +3989 -0
- data/lib/bel_parser/parsers/expression/term.rl +157 -0
- data/lib/bel_parser/parsers/line_parser.rb +92 -0
- data/lib/bel_parser/parsers/mixin/buffer.rb +10 -0
- data/lib/bel_parser/parsers/nonblocking_io_wrapper.rb +50 -0
- data/lib/bel_parser/parsers/serializer.rb +205 -0
- data/lib/bel_parser/quoting.rb +177 -0
- data/lib/bel_parser/resource/concept.rb +56 -0
- data/lib/bel_parser/resource/concept_scheme.rb +35 -0
- data/lib/bel_parser/resource/dataset.rb +34 -0
- data/lib/bel_parser/resource/eager_reader.rb +89 -0
- data/lib/bel_parser/resource/eager_sparql_reader.rb +51 -0
- data/lib/bel_parser/resource/file_resource.rb +21 -0
- data/lib/bel_parser/resource/file_resource_value.rb +24 -0
- data/lib/bel_parser/resource/jena_tdb_reader.rb +246 -0
- data/lib/bel_parser/resource/lru_cache.rb +111 -0
- data/lib/bel_parser/resource/lru_reader.rb +34 -0
- data/lib/bel_parser/resource/reader.rb +18 -0
- data/lib/bel_parser/resource/resource_url_reader.rb +181 -0
- data/lib/bel_parser/resource/sparql_reader.rb +179 -0
- data/lib/bel_parser/resource/value.rb +31 -0
- data/lib/bel_parser/script.rb +8 -0
- data/lib/bel_parser/script/filter.rb +35 -0
- data/lib/bel_parser/script/first_node.rb +21 -0
- data/lib/bel_parser/script/keywords.rb +32 -0
- data/lib/bel_parser/script/nanopub_mapper.rb +182 -0
- data/lib/bel_parser/script/parser.rb +51 -0
- data/lib/bel_parser/script/state/annotation_definition.rb +62 -0
- data/lib/bel_parser/script/state/bel_version.rb +36 -0
- data/lib/bel_parser/script/state/document_property.rb +29 -0
- data/lib/bel_parser/script/state/namespace_definition.rb +32 -0
- data/lib/bel_parser/script/state/set.rb +82 -0
- data/lib/bel_parser/script/state/unset.rb +46 -0
- data/lib/bel_parser/script/state_aggregator.rb +49 -0
- data/lib/bel_parser/script/state_function.rb +10 -0
- data/lib/bel_parser/script/syntax/expression_validation.rb +46 -0
- data/lib/bel_parser/script/syntax/invalid_regex_pattern.rb +49 -0
- data/lib/bel_parser/script/syntax/undefined_annotation.rb +61 -0
- data/lib/bel_parser/script/syntax/undefined_annotation_value.rb +84 -0
- data/lib/bel_parser/script/syntax/unresolvable_namespace.rb +54 -0
- data/lib/bel_parser/script/syntax/unsupported_bel_version.rb +59 -0
- data/lib/bel_parser/script/validator.rb +65 -0
- data/lib/bel_parser/vendor/ast.rb +17 -0
- data/lib/bel_parser/vendor/ast/node.rb +254 -0
- data/lib/bel_parser/vendor/ast/processor.rb +12 -0
- data/lib/bel_parser/vendor/ast/processor/mixin.rb +282 -0
- data/lib/bel_parser/vendor/ast/sexp.rb +30 -0
- metadata +390 -0
@@ -0,0 +1,146 @@
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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 'identifier.rl';
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include 'string.rl';
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action clear {
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@buffers.delete(:string)
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@buffers.delete(:ident)
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}
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action string {
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@buffers[:list_arg] = list_item(@buffers[:string])
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}
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action ident {
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@buffers[:list_arg] = list_item(@buffers[:ident])
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}
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action start_list {
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@buffers[:list] = list()
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}
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action append_list {
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# Append list argument if its value is not empty.
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if @buffers[:list_arg]
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list_arg_value = @buffers[:list_arg].children[0].children[0]
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if list_arg_value != ''
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@buffers[:list] <<= @buffers[:list_arg]
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end
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end
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}
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action finish_list {
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#TODO: Mark @buffers[:list] as complete.
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}
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action error_list_string {
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#TODO: Mark @buffers[:list_arg] string as error.
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@buffers[:list_arg] = list_item(@buffers[:string])
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}
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action error_list_ident {
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#TODO: Mark @buffers[:list_arg] identifier as error.
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@buffers[:list_arg] = list_item(@buffers[:ident])
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}
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action yield_complete_list {
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yield @buffers[:list]
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}
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action yield_error_list {
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@buffers[:list] ||= list()
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yield @buffers[:list]
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}
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LIST =
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'{' @start_list
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SP*
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(
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STRING %string $err(error_list_string) |
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IDENT %ident $err(error_list_ident)
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)? $err(append_list) %append_list
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SP*
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(
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',' @clear
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SP*
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(
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STRING %string $err(error_list_string) |
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IDENT %ident $err(error_list_ident)
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) $err(append_list) %append_list
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SP*
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)*
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'}' @finish_list;
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list := LIST $err(yield_error_list) %yield_complete_list NL;
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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 Common
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module List
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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::Common::List.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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@@ -0,0 +1,271 @@
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# begin: ragel
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=begin
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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 Common
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module String
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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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class << self
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attr_accessor :_bel_trans_keys
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private :_bel_trans_keys, :_bel_trans_keys=
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end
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self._bel_trans_keys = [
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0, 0, 34, 34, 34, 92,
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10, 10, 92, 92, 0,
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0, 0
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]
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class << self
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attr_accessor :_bel_key_spans
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private :_bel_key_spans, :_bel_key_spans=
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end
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self._bel_key_spans = [
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0, 1, 59, 1, 1, 0
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]
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class << self
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attr_accessor :_bel_index_offsets
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private :_bel_index_offsets, :_bel_index_offsets=
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end
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self._bel_index_offsets = [
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0, 0, 2, 62, 64, 66
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]
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class << self
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attr_accessor :_bel_indicies
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private :_bel_indicies, :_bel_indicies=
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end
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self._bel_indicies = [
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1, 0, 3, 2, 2, 2, 2, 2,
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2, 2, 2, 2, 2, 2, 2, 2,
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75
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2, 2, 2, 2, 2, 2, 2, 2,
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2, 2, 2, 2, 2, 2, 2, 2,
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2, 2, 2, 2, 2, 2, 2, 2,
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78
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2, 2, 2, 2, 2, 2, 2, 2,
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2, 2, 2, 2, 2, 2, 2, 2,
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2, 2, 2, 2, 4, 2, 5, 0,
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4, 2, 6, 0
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]
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class << self
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attr_accessor :_bel_trans_targs
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private :_bel_trans_targs, :_bel_trans_targs=
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end
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self._bel_trans_targs = [
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0, 2, 2, 3, 4, 5, 0
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90
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]
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class << self
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attr_accessor :_bel_trans_actions
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private :_bel_trans_actions, :_bel_trans_actions=
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end
|
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self._bel_trans_actions = [
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1, 2, 3, 3, 3, 4, 0
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]
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class << self
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attr_accessor :_bel_eof_actions
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private :_bel_eof_actions, :_bel_eof_actions=
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end
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self._bel_eof_actions = [
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0, 1, 1, 1, 1, 0
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]
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+
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class << self
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attr_accessor :bel_start
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end
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self.bel_start = 1;
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class << self
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attr_accessor :bel_first_final
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end
|
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self.bel_first_final = 5;
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class << self
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attr_accessor :bel_error
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end
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self.bel_error = 0;
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+
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class << self
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attr_accessor :bel_en_string
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end
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self.bel_en_string = 1;
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+
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+
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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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+
|
137
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# begin: ragel
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138
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+
|
139
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begin
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p ||= 0
|
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pe ||= data.length
|
142
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cs = bel_start
|
143
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+
end
|
144
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+
|
145
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+
|
146
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+
begin
|
147
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testEof = false
|
148
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_slen, _trans, _keys, _inds, _acts, _nacts = nil
|
149
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_goto_level = 0
|
150
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_resume = 10
|
151
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_eof_trans = 15
|
152
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_again = 20
|
153
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_test_eof = 30
|
154
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+
_out = 40
|
155
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+
while true
|
156
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if _goto_level <= 0
|
157
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+
if p == pe
|
158
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+
_goto_level = _test_eof
|
159
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+
next
|
160
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+
end
|
161
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+
if cs == 0
|
162
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+
_goto_level = _out
|
163
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+
next
|
164
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+
end
|
165
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+
end
|
166
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+
if _goto_level <= _resume
|
167
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+
_keys = cs << 1
|
168
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+
_inds = _bel_index_offsets[cs]
|
169
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+
_slen = _bel_key_spans[cs]
|
170
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+
_wide = data[p].ord
|
171
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+
_trans = if ( _slen > 0 &&
|
172
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_bel_trans_keys[_keys] <= _wide &&
|
173
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_wide <= _bel_trans_keys[_keys + 1]
|
174
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+
) then
|
175
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_bel_indicies[ _inds + _wide - _bel_trans_keys[_keys] ]
|
176
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else
|
177
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+
_bel_indicies[ _inds + _slen ]
|
178
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+
end
|
179
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+
cs = _bel_trans_targs[_trans]
|
180
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+
if _bel_trans_actions[_trans] != 0
|
181
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+
case _bel_trans_actions[_trans]
|
182
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+
when 3 then
|
183
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+
begin
|
184
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+
|
185
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+
(@buffers[:string] ||= []) << data[p].ord
|
186
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+
end
|
187
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+
when 2 then
|
188
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+
begin
|
189
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+
|
190
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+
@buffers[:string] = []
|
191
|
+
end
|
192
|
+
begin
|
193
|
+
|
194
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+
(@buffers[:string] ||= []) << data[p].ord
|
195
|
+
end
|
196
|
+
when 4 then
|
197
|
+
begin
|
198
|
+
|
199
|
+
@buffers[:string] = string(utf8_string(@buffers[:string]))
|
200
|
+
end
|
201
|
+
begin
|
202
|
+
|
203
|
+
yield @buffers[:string]
|
204
|
+
end
|
205
|
+
when 1 then
|
206
|
+
begin
|
207
|
+
|
208
|
+
@buffers[:string] ||= []
|
209
|
+
@buffers[:string] = string(utf8_string(@buffers[:string]).sub(/\n$/, ''))
|
210
|
+
end
|
211
|
+
begin
|
212
|
+
|
213
|
+
@buffers[:string] ||= []
|
214
|
+
yield @buffers[:string]
|
215
|
+
end
|
216
|
+
end
|
217
|
+
end
|
218
|
+
end
|
219
|
+
if _goto_level <= _again
|
220
|
+
if cs == 0
|
221
|
+
_goto_level = _out
|
222
|
+
next
|
223
|
+
end
|
224
|
+
p += 1
|
225
|
+
if p != pe
|
226
|
+
_goto_level = _resume
|
227
|
+
next
|
228
|
+
end
|
229
|
+
end
|
230
|
+
if _goto_level <= _test_eof
|
231
|
+
if p == eof
|
232
|
+
case _bel_eof_actions[cs]
|
233
|
+
when 1 then
|
234
|
+
begin
|
235
|
+
|
236
|
+
@buffers[:string] ||= []
|
237
|
+
@buffers[:string] = string(utf8_string(@buffers[:string]).sub(/\n$/, ''))
|
238
|
+
end
|
239
|
+
begin
|
240
|
+
|
241
|
+
@buffers[:string] ||= []
|
242
|
+
yield @buffers[:string]
|
243
|
+
end
|
244
|
+
end
|
245
|
+
end
|
246
|
+
|
247
|
+
end
|
248
|
+
if _goto_level <= _out
|
249
|
+
break
|
250
|
+
end
|
251
|
+
end
|
252
|
+
end
|
253
|
+
|
254
|
+
# end: ragel
|
255
|
+
end
|
256
|
+
end
|
257
|
+
end
|
258
|
+
end
|
259
|
+
end
|
260
|
+
end
|
261
|
+
|
262
|
+
if __FILE__ == $0
|
263
|
+
$stdin.each_line do |line|
|
264
|
+
BELParser::Parsers::Common::String.parse(line) { |obj|
|
265
|
+
puts obj.inspect
|
266
|
+
}
|
267
|
+
end
|
268
|
+
end
|
269
|
+
|
270
|
+
# vim: ft=ruby ts=2 sw=2:
|
271
|
+
# encoding: utf-8
|
@@ -0,0 +1,107 @@
|
|
1
|
+
# begin: ragel
|
2
|
+
=begin
|
3
|
+
%%{
|
4
|
+
machine bel;
|
5
|
+
|
6
|
+
include 'common.rl';
|
7
|
+
|
8
|
+
action start_string {
|
9
|
+
@buffers[:string] = []
|
10
|
+
}
|
11
|
+
|
12
|
+
action append_string {
|
13
|
+
(@buffers[:string] ||= []) << fc
|
14
|
+
}
|
15
|
+
|
16
|
+
action finish_string {
|
17
|
+
@buffers[:string] = string(utf8_string(@buffers[:string]))
|
18
|
+
}
|
19
|
+
|
20
|
+
action error_string {
|
21
|
+
@buffers[:string] ||= []
|
22
|
+
@buffers[:string] = string(utf8_string(@buffers[:string]).sub(/\n$/, ''))
|
23
|
+
}
|
24
|
+
|
25
|
+
action yield_complete_string {
|
26
|
+
yield @buffers[:string]
|
27
|
+
}
|
28
|
+
|
29
|
+
action yield_error_string {
|
30
|
+
@buffers[:string] ||= []
|
31
|
+
yield @buffers[:string]
|
32
|
+
}
|
33
|
+
|
34
|
+
STRING =
|
35
|
+
('"' ('\\\"' | [^"])** '"') >start_string $append_string %finish_string $err(error_string);
|
36
|
+
|
37
|
+
string :=
|
38
|
+
STRING $err(yield_error_string) %yield_complete_string
|
39
|
+
NL;
|
40
|
+
}%%
|
41
|
+
=end
|
42
|
+
# end: ragel
|
43
|
+
|
44
|
+
require_relative '../ast/node'
|
45
|
+
require_relative '../mixin/buffer'
|
46
|
+
require_relative '../nonblocking_io_wrapper'
|
47
|
+
|
48
|
+
module BELParser
|
49
|
+
module Parsers
|
50
|
+
module Common
|
51
|
+
module String
|
52
|
+
|
53
|
+
class << self
|
54
|
+
|
55
|
+
MAX_LENGTH = 1024 * 128 # 128K
|
56
|
+
|
57
|
+
def parse(content)
|
58
|
+
return nil unless content
|
59
|
+
|
60
|
+
Parser.new(content).each do |obj|
|
61
|
+
yield obj
|
62
|
+
end
|
63
|
+
end
|
64
|
+
end
|
65
|
+
|
66
|
+
private
|
67
|
+
|
68
|
+
class Parser
|
69
|
+
include Enumerable
|
70
|
+
include BELParser::Parsers::Buffer
|
71
|
+
include BELParser::Parsers::AST::Sexp
|
72
|
+
|
73
|
+
def initialize(content)
|
74
|
+
@content = content
|
75
|
+
# begin: ragel
|
76
|
+
%% write data;
|
77
|
+
# end: ragel
|
78
|
+
end
|
79
|
+
|
80
|
+
def each
|
81
|
+
@buffers = {}
|
82
|
+
data = @content.unpack('C*')
|
83
|
+
p = 0
|
84
|
+
pe = data.length
|
85
|
+
eof = data.length
|
86
|
+
|
87
|
+
# begin: ragel
|
88
|
+
%% write init;
|
89
|
+
%% write exec;
|
90
|
+
# end: ragel
|
91
|
+
end
|
92
|
+
end
|
93
|
+
end
|
94
|
+
end
|
95
|
+
end
|
96
|
+
end
|
97
|
+
|
98
|
+
if __FILE__ == $0
|
99
|
+
$stdin.each_line do |line|
|
100
|
+
BELParser::Parsers::Common::String.parse(line) { |obj|
|
101
|
+
puts obj.inspect
|
102
|
+
}
|
103
|
+
end
|
104
|
+
end
|
105
|
+
|
106
|
+
# vim: ft=ruby ts=2 sw=2:
|
107
|
+
# encoding: utf-8
|