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 +1,38 @@
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module BEL::Translator::Plugins
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# BELScript plugs a translator for BEL Script into bel.rb.
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# Supports multiple BEL specifications by using the
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# {BELParser::Language::ExpressionValidator expression validator}.
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module BelScript
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ID = :bel_script
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NAME = 'BEL Script Translator'
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DESCRIPTION = 'A translator that reads/writes BEL nanopubs to BEL Script.'
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MEDIA_TYPES = %i(application/bel)
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EXTENSIONS = %i(bel)
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def self.create_translator(options = {})
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require 'bel'
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require_relative 'bel_script/translator'
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BelScriptTranslator.new
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end
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def self.id
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ID
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end
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def self.name
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NAME
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end
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def self.description
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DESCRIPTION
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end
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def self.media_types
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MEDIA_TYPES
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end
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def self.file_extensions
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EXTENSIONS
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end
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end
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end
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require_relative 'nanopub_serialization.rb'
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# BEL Script nanopub serialization that groups nanopub by citation scoped to
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# individual statement groups (i.e. BEL Script's +SET STATEMENT_GROUP+ and
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# +UNSET STATEMENT_GROUP+).
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#
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# @example Citation serialization for a group of nanopub
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# SET STATEMENT_GROUP = 12857727
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# SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
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# SET Support = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
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# SET CellLine = "MCF 10A"
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# SET TextLocation = Abstract
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# complex(p(HGNC:USF1),g(HGNC:IGF2R))
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#
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# complex(p(HGNC:USF2),g(HGNC:IGF2R))
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#
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# tscript(p(HGNC:USF2)) directlyIncreases r(HGNC:IGF2R)
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#
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# tscript(p(HGNC:USF1)) causesNoChange r(HGNC:IGF2R)
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#
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# SET Support = "c-Myc was present on the CDK4 promoter to the ..."
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# complex(p(HGNC:MYC),g(HGNC:CDK4))
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# UNSET STATEMENT_GROUP
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module BEL::Translator::Plugins::BelScript::BelCitationSerialization
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include BEL::Translator::Plugins::BelScript::NanopubSerialization
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# Serialize the {BEL::Nanopub::Nanopub nanopub} to a BEL Script string.
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#
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# Includes +SET AnnotationName+ and +UNSET AnnotationName+ where needed in
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# order to remove duplicating annotations.
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#
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# @param [BEL::Nanopub::Nanopub] nanopub the nanopub to serialize
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# @return [String] the BEL Script string
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def to_bel(nanopub)
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bel = ''
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citation = citation_value(nanopub)
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support = support_value(nanopub)
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annotations = annotation_values(nanopub)
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current_annotations = {}.merge(annotations)
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current_annotations[:Citation] = citation if citation
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current_annotations[:Support] = support if support
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if !nanopub.citation.id || nanopub.citation.id.empty?
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citation_id = quote('')
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else
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citation_id = quote_if_needed(nanopub.citation.id)
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end
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# Reset cumulative annotations if new citation.
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if cumulative_citation == nil
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bel << %Q{SET STATEMENT_GROUP = #{citation_id}\n}
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cumulative_annotations.clear
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elsif nanopub.citation != cumulative_citation
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bel << %Q{UNSET STATEMENT_GROUP\n}
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bel << "\n\n"
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bel << %Q{SET STATEMENT_GROUP = #{citation_id}\n}
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cumulative_annotations.clear
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end
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# Hang on to the last citation.
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self.cumulative_citation = nanopub.citation
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# UNSET unused annotations from previous nanopub.
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(cumulative_annotations.keys - current_annotations.keys).each do |unset_key|
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bel << "UNSET #{unset_key}\n"
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cumulative_annotations.delete(unset_key)
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end
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# Remove annotation if key/value was SET by a previous nanopub.
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Hash[
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cumulative_annotations.to_a & current_annotations.to_a
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].each do |same_k, _|
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current_annotations.delete(same_k)
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end
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# Retain the current nanopub's annotation in cumulative set.
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cumulative_annotations.merge!(current_annotations)
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# SET Citation
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citation = current_annotations.delete(:Citation)
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if citation
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bel << "SET Citation = {#{citation}}\n"
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end
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# SET Support
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support = current_annotations.delete(:Support)
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if support
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bel << %Q{SET Support = "#{support}"\n}
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end
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# SET new or modified annotations
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current_annotations.sort.each do |(name, value)|
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bel << "SET #{name} = #{value}\n"
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end
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# Assert BEL statement
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bel << "#{nanopub.bel_statement}\n"
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# Separate nanopub by new line.
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bel << "\n"
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bel
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end
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private
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# The cumulative citation that is active for the current nanopub. This is
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# tracked in order to decide when to begin a new statement group.
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attr_accessor :cumulative_citation
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# Returns the cumulative +Hash+ of annotations. This *state* is used to keep
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# track of the active, scoped annotations as nanopub is serialized.
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def cumulative_annotations
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@cumulative_annotations ||= {}
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end
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# Return BEL Script syntax that should completes the BEL Script document.
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# For Citation serialization we will always end with the unset of a
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# statement group.
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def epilogue
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%Q{UNSET STATEMENT_GROUP\n}
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end
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end
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require_relative 'nanopub_serialization'
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# BEL Script nanopub serialization that writes each nanopub with their full
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# set of annotations (i.e. includes all `SET` and necessary `UNSET` records).
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# This style is more readable because it groups all set annotations near the
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# BEL statement.
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#
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# @example Discrete serialization for a group of nanopub
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# SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
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# SET Support = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
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# SET CellLine = "MCF 10A"
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# SET TextLocation = Abstract
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# complex(p(HGNC:USF1),g(HGNC:IGF2R))
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#
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# SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
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# SET Support = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
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# SET CellLine = "MCF 10A"
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# SET TextLocation = Abstract
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# complex(p(HGNC:USF2),g(HGNC:IGF2R))
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#
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# SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
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# SET Support = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
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# SET CellLine = "MCF 10A"
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# SET TextLocation = Abstract
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# tscript(p(HGNC:USF2)) directlyIncreases r(HGNC:IGF2R)
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#
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# SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
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# SET Support = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
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# SET CellLine = "MCF 10A"
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# SET TextLocation = Abstract
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# tscript(p(HGNC:USF1)) causesNoChange r(HGNC:IGF2R)
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#
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# SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
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# SET Support = "c-Myc was present on the CDK4 promoter to the ..."
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# SET CellLine = "MCF 10A"
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# SET TextLocation = Abstract
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# complex(p(HGNC:MYC),g(HGNC:CDK4))
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#
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# UNSET CellLine
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module BEL::Translator::Plugins::BelScript::BelDiscreteSerialization
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include BEL::Translator::Plugins::BelScript::NanopubSerialization
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# Serialize the {BEL::Nanopub::Nanopub nanopub} to a BEL Script string.
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# Includes all necessary +SET AnnotationName+ and +UNSET AnnotationName+
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# records around the BEL statement.
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#
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# @param [BEL::Nanopub::Nanopub] nanopub the nanopub to serialize
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# @return [String] the BEL Script string
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def to_bel(nanopub)
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bel = ''
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citation = citation_value(nanopub)
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support = support_value(nanopub)
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annotations = annotation_values(nanopub)
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current_annotations = {}.merge(annotations)
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current_annotations[:Citation] = citation if citation
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current_annotations[:Support] = support if support
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# UNSET unused annotations from previous nanopub.
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(cumulative_annotations.keys - current_annotations.keys).each do |unset_key|
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bel << "UNSET #{unset_key}\n"
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cumulative_annotations.delete(unset_key)
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end
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# Retain the current nanopub's annotation in cumulative set.
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cumulative_annotations.merge!(current_annotations)
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# SET Citation
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citation = current_annotations.delete(:Citation)
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if citation
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bel << "SET Citation = {#{citation}}\n"
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end
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# SET Support
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support = current_annotations.delete(:Support)
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if support
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bel << %Q{SET Support = "#{support}"\n}
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end
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# SET new or modified annotations
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current_annotations.sort.each do |(name, value)|
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bel << "SET #{name} = #{value}\n"
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end
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# Assert BEL statement
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bel << "#{nanopub.bel_statement}\n"
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# Separate nanopub by new line.
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bel << "\n"
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bel
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end
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|
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private
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|
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# Returns the cumulative +Hash+ of annotations. This *state* is used to keep
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# track of the active, scoped annotations as nanopub is serialized.
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def cumulative_annotations
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@cumulative_annotations ||= {}
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end
|
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|
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# Return BEL Script syntax that completes the BEL Script document.
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# The empty string is returned since no ending syntax is necessary when
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# serializing each nanopub discretely.
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def epilogue
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""
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end
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end
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@@ -0,0 +1,100 @@
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require_relative 'nanopub_serialization.rb'
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# BEL Script nanopub serialization that writes nanopubs sequentially while
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# including only the necessary unsetting of annotations (i.e. BEL Script's
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# +UNSET AnnotationName+ syntax).
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#
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# @example Top-down serialization for a group of nanopubs
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# SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
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# SET Support = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
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# SET CellLine = "MCF 10A"
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# SET TextLocation = Abstract
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# complex(p(HGNC:USF1),g(HGNC:IGF2R))
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#
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# complex(p(HGNC:USF2),g(HGNC:IGF2R))
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15
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#
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# tscript(p(HGNC:USF2)) directlyIncreases r(HGNC:IGF2R)
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#
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# tscript(p(HGNC:USF1)) causesNoChange r(HGNC:IGF2R)
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19
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#
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20
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# SET Support = "c-Myc was present on the CDK4 promoter to the ..."
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21
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# complex(p(HGNC:MYC),g(HGNC:CDK4))
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22
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#
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23
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# UNSET CellLine
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24
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module BEL::Translator::Plugins::BelScript::BelTopDownSerialization
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25
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include BEL::Translator::Plugins::BelScript::NanopubSerialization
|
26
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|
27
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# Serialize the {BEL::Nanopub::Nanopub nanopub} to a BEL Script string.
|
28
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# Includes all necessary +SET AnnotationName+ and +UNSET AnnotationName+
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29
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# records within the scope of a citation's statement group.
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30
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#
|
31
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# @param [BEL::Nanopub::Nanopub] nanopub the nanopub to serialize
|
32
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# @return [String] the BEL Script string
|
33
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def to_bel(nanopub)
|
34
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bel = ''
|
35
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+
|
36
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citation = citation_value(nanopub)
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37
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support = support_value(nanopub)
|
38
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annotations = annotation_values(nanopub)
|
39
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+
|
40
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current_annotations = {}.merge(annotations)
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41
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current_annotations[:Citation] = citation if citation
|
42
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current_annotations[:Support] = support if support
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43
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+
|
44
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# UNSET unused annotations from previous nanopub.
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45
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(cumulative_annotations.keys - current_annotations.keys).each do |unset_key|
|
46
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bel << "UNSET #{unset_key}\n"
|
47
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cumulative_annotations.delete(unset_key)
|
48
|
+
end
|
49
|
+
|
50
|
+
# Remove annotation if key/value was SET by a previous nanopub.
|
51
|
+
Hash[
|
52
|
+
cumulative_annotations.to_a & current_annotations.to_a
|
53
|
+
].each do |same_k, _|
|
54
|
+
current_annotations.delete(same_k)
|
55
|
+
end
|
56
|
+
|
57
|
+
# Retain the current nanopub's annotation in cumulative set.
|
58
|
+
cumulative_annotations.merge!(current_annotations)
|
59
|
+
|
60
|
+
# SET Citation
|
61
|
+
citation = current_annotations.delete(:Citation)
|
62
|
+
if citation
|
63
|
+
bel << "SET Citation = {#{citation}}\n"
|
64
|
+
end
|
65
|
+
|
66
|
+
# SET Support
|
67
|
+
support = current_annotations.delete(:Support)
|
68
|
+
if support
|
69
|
+
bel << %Q{SET Support = "#{support}"\n}
|
70
|
+
end
|
71
|
+
|
72
|
+
# SET new or modified annotations
|
73
|
+
current_annotations.sort.each do |(name, value)|
|
74
|
+
bel << "SET #{name} = #{value}\n"
|
75
|
+
end
|
76
|
+
|
77
|
+
# Assert BEL statement
|
78
|
+
bel << "#{nanopub.bel_statement}\n"
|
79
|
+
|
80
|
+
# Separate nanopub by new line.
|
81
|
+
bel << "\n"
|
82
|
+
|
83
|
+
bel
|
84
|
+
end
|
85
|
+
|
86
|
+
private
|
87
|
+
|
88
|
+
# Returns the cumulative +Hash+ of annotations. This *state* is used to keep
|
89
|
+
# track of the active, scoped annotations as nanopub is serialized.
|
90
|
+
def cumulative_annotations
|
91
|
+
@cumulative_annotations ||= {}
|
92
|
+
end
|
93
|
+
|
94
|
+
# Return BEL Script syntax that completes the BEL Script document.
|
95
|
+
# The empty string is returned since no ending syntax is necessary when
|
96
|
+
# serializing in a top-down manner.
|
97
|
+
def epilogue
|
98
|
+
""
|
99
|
+
end
|
100
|
+
end
|
@@ -0,0 +1,79 @@
|
|
1
|
+
require 'bel/quoting'
|
2
|
+
|
3
|
+
# Serializing of common {BEL::Nanopub::Nanopub nanopub} components to BEL
|
4
|
+
# Script syntax.
|
5
|
+
#
|
6
|
+
# @abstract
|
7
|
+
module BEL::Translator::Plugins::BelScript::NanopubSerialization
|
8
|
+
include BEL::Quoting
|
9
|
+
|
10
|
+
# Serialize the {BEL::Nanopub::Nanopub nanopub} to a BEL Script string.
|
11
|
+
#
|
12
|
+
# @param [BEL::Nanopub::Nanopub] nanopub the nanopub to serialize
|
13
|
+
# @return [String] the BEL Script string
|
14
|
+
# @abstract Include and override {#to_bel} to implement serialization
|
15
|
+
# {BEL::Nanopub::Nanopub nanopub} to BEL Script
|
16
|
+
def to_bel(nanopub)
|
17
|
+
end
|
18
|
+
|
19
|
+
# Return BEL Script syntax that completes the BEL Script document.
|
20
|
+
#
|
21
|
+
# @abstract
|
22
|
+
def epilogue
|
23
|
+
raise NotImplementedError.new("#{self.class}#epilogue")
|
24
|
+
end
|
25
|
+
|
26
|
+
protected
|
27
|
+
|
28
|
+
def citation_value(nanopub)
|
29
|
+
citation = nanopub.citation
|
30
|
+
|
31
|
+
return nil unless citation && citation.valid?
|
32
|
+
|
33
|
+
values = citation.to_a
|
34
|
+
values.map! { |v|
|
35
|
+
v ||= ""
|
36
|
+
if v.respond_to?(:each)
|
37
|
+
%Q{"#{v.join('|')}"}
|
38
|
+
else
|
39
|
+
%Q{"#{v}"}
|
40
|
+
end
|
41
|
+
}
|
42
|
+
values.join(', ')
|
43
|
+
end
|
44
|
+
|
45
|
+
def support_value(nanopub)
|
46
|
+
support = nanopub.support
|
47
|
+
|
48
|
+
return nil unless support && support.value
|
49
|
+
|
50
|
+
value = support.value
|
51
|
+
value.gsub!("\n", "")
|
52
|
+
value.gsub!('"', %Q{\\"})
|
53
|
+
value
|
54
|
+
end
|
55
|
+
|
56
|
+
def annotation_values(nanopub)
|
57
|
+
experiment_context = nanopub.experiment_context
|
58
|
+
|
59
|
+
return {} unless experiment_context
|
60
|
+
|
61
|
+
Hash[
|
62
|
+
experiment_context.
|
63
|
+
sort_by { |obj| obj[:name].to_sym }.
|
64
|
+
map { |obj|
|
65
|
+
name = obj[:name].to_sym
|
66
|
+
value = obj[:value]
|
67
|
+
|
68
|
+
value_s =
|
69
|
+
if value.respond_to? :map
|
70
|
+
"{#{value.map { |v| quote(v) }.join(', ')}}"
|
71
|
+
else
|
72
|
+
quote(value)
|
73
|
+
end
|
74
|
+
|
75
|
+
[name, value_s]
|
76
|
+
}
|
77
|
+
]
|
78
|
+
end
|
79
|
+
end
|