bel_parser 1.0.0.alpha.27-java

data/lib/bel_parser/vendor/ast/sexp.rb

@@ -0,0 +1,30 @@
+module AST
+  # This simple module is very useful in the cases where one needs
+  # to define deeply nested ASTs from Ruby code, for example, in
+  # tests. It should be used like this:
+  #
+  #     describe YourLanguage::AST do
+  #       include Sexp
+  #
+  #       it "should correctly parse expressions" do
+  #         YourLanguage.parse("1 + 2 * 3").should ==
+  #             s(:add,
+  #               s(:integer, 1),
+  #               s(:multiply,
+  #                 s(:integer, 2),
+  #                 s(:integer, 3)))
+  #       end
+  #     end
+  #
+  # This way the amount of boilerplate code is greatly reduced.
+  module Sexp
+    # Creates a {Node} with type `type` and children `children`.
+    # Note that the resulting node is of the type AST::Node and not a
+    # subclass.
+    # This would not pose a problem with comparisons, as {Node#==}
+    # ignores metadata.
+    def s(type, *children)
+      Node.new(type, children)
+    end
+  end
+end

metadata

@@ -0,0 +1,390 @@
+--- !ruby/object:Gem::Specification
+name: bel_parser
+version: !ruby/object:Gem::Version
+  version: 1.0.0.alpha.27
+platform: java
+authors:
+- Anthony Bargnesi
+- Nick Bargnesi
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2016-05-09 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.6.0.beta
+  name: dbm-mapdb3
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.6.0.beta
+description: Implements language versions 1.0 and 2.0.
+email: abargnesi@selventa.com
+executables:
+- bel2_validator
+- bel_script_reader
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gemspec-java"
+- CHANGELOG.md
+- LICENSE
+- README.md
+- VERSION
+- bin/bel2_validator
+- bin/bel_script_reader
+- lib/bel/translator/plugins/bel_script.rb
+- lib/bel/translator/plugins/bel_script/bel_citation_serialization.rb
+- lib/bel/translator/plugins/bel_script/bel_discrete_serialization.rb
+- lib/bel/translator/plugins/bel_script/bel_top_down_serialization.rb
+- lib/bel/translator/plugins/bel_script/nanopub_serialization.rb
+- lib/bel/translator/plugins/bel_script/reader.rb
+- lib/bel/translator/plugins/bel_script/translator.rb
+- lib/bel/translator/plugins/bel_script/writer.rb
+- lib/bel_parser.rb
+- lib/bel_parser/ast_filter.rb
+- lib/bel_parser/ast_generator.rb
+- lib/bel_parser/expression.rb
+- lib/bel_parser/expression/filter.rb
+- lib/bel_parser/expression/parser.rb
+- lib/bel_parser/expression/validator.rb
+- lib/bel_parser/language.rb
+- lib/bel_parser/language/amino_acid.rb
+- lib/bel_parser/language/apply_namespace_encoding.rb
+- lib/bel_parser/language/base_specification.rb
+- lib/bel_parser/language/covalent_protein_modification.rb
+- lib/bel_parser/language/expression_validator.rb
+- lib/bel_parser/language/function.rb
+- lib/bel_parser/language/relationship.rb
+- lib/bel_parser/language/semantics.rb
+- lib/bel_parser/language/semantics/deeply_nested_statement.rb
+- lib/bel_parser/language/semantics/function_deprecation.rb
+- lib/bel_parser/language/semantics/list_function_subject.rb
+- lib/bel_parser/language/semantics/multiple_subject_object.rb
+- lib/bel_parser/language/semantics/non_causal_nested_statement.rb
+- lib/bel_parser/language/semantics/non_object_list.rb
+- lib/bel_parser/language/semantics/relationship_deprecation.rb
+- lib/bel_parser/language/semantics/relationship_not_listable.rb
+- lib/bel_parser/language/semantics/signature_mapping.rb
+- lib/bel_parser/language/semantics_ast.rb
+- lib/bel_parser/language/semantics_ast_warnings.rb
+- lib/bel_parser/language/semantics_function.rb
+- lib/bel_parser/language/semantics_match.rb
+- lib/bel_parser/language/semantics_result.rb
+- lib/bel_parser/language/semantics_type_warning.rb
+- lib/bel_parser/language/semantics_warning.rb
+- lib/bel_parser/language/signature.rb
+- lib/bel_parser/language/specification.rb
+- lib/bel_parser/language/syntax.rb
+- lib/bel_parser/language/syntax/invalid_function.rb
+- lib/bel_parser/language/syntax/invalid_relationship.rb
+- lib/bel_parser/language/syntax/undefined_namespace.rb
+- lib/bel_parser/language/syntax/undefined_namespace_value.rb
+- lib/bel_parser/language/syntax_error.rb
+- lib/bel_parser/language/syntax_function.rb
+- lib/bel_parser/language/syntax_result.rb
+- lib/bel_parser/language/syntax_warning.rb
+- lib/bel_parser/language/version1_0.rb
+- lib/bel_parser/language/version1_0/functions/abundance.rb
+- lib/bel_parser/language/version1_0/functions/biological_process.rb
+- lib/bel_parser/language/version1_0/functions/catalytic_activity.rb
+- lib/bel_parser/language/version1_0/functions/cell_secretion.rb
+- lib/bel_parser/language/version1_0/functions/cell_surface_expression.rb
+- lib/bel_parser/language/version1_0/functions/chaperone_activity.rb
+- lib/bel_parser/language/version1_0/functions/complex_abundance.rb
+- lib/bel_parser/language/version1_0/functions/composite_abundance.rb
+- lib/bel_parser/language/version1_0/functions/degradation.rb
+- lib/bel_parser/language/version1_0/functions/fusion.rb
+- lib/bel_parser/language/version1_0/functions/gene_abundance.rb
+- lib/bel_parser/language/version1_0/functions/gtp_bound_activity.rb
+- lib/bel_parser/language/version1_0/functions/kinase_activity.rb
+- lib/bel_parser/language/version1_0/functions/list.rb
+- lib/bel_parser/language/version1_0/functions/micro_rna_abundance.rb
+- lib/bel_parser/language/version1_0/functions/molecular_activity.rb
+- lib/bel_parser/language/version1_0/functions/pathology.rb
+- lib/bel_parser/language/version1_0/functions/peptidase_activity.rb
+- lib/bel_parser/language/version1_0/functions/phosphatase_activity.rb
+- lib/bel_parser/language/version1_0/functions/products.rb
+- lib/bel_parser/language/version1_0/functions/protein_abundance.rb
+- lib/bel_parser/language/version1_0/functions/protein_modification.rb
+- lib/bel_parser/language/version1_0/functions/reactants.rb
+- lib/bel_parser/language/version1_0/functions/reaction.rb
+- lib/bel_parser/language/version1_0/functions/ribosylation_activity.rb
+- lib/bel_parser/language/version1_0/functions/rna_abundance.rb
+- lib/bel_parser/language/version1_0/functions/substitution.rb
+- lib/bel_parser/language/version1_0/functions/transcriptional_activity.rb
+- lib/bel_parser/language/version1_0/functions/translocation.rb
+- lib/bel_parser/language/version1_0/functions/transport_activity.rb
+- lib/bel_parser/language/version1_0/functions/truncation.rb
+- lib/bel_parser/language/version1_0/relationships/acts_in.rb
+- lib/bel_parser/language/version1_0/relationships/analogous.rb
+- lib/bel_parser/language/version1_0/relationships/association.rb
+- lib/bel_parser/language/version1_0/relationships/biomarker_for.rb
+- lib/bel_parser/language/version1_0/relationships/causes_no_change.rb
+- lib/bel_parser/language/version1_0/relationships/decreases.rb
+- lib/bel_parser/language/version1_0/relationships/directly_decreases.rb
+- lib/bel_parser/language/version1_0/relationships/directly_increases.rb
+- lib/bel_parser/language/version1_0/relationships/has_component.rb
+- lib/bel_parser/language/version1_0/relationships/has_components.rb
+- lib/bel_parser/language/version1_0/relationships/has_member.rb
+- lib/bel_parser/language/version1_0/relationships/has_members.rb
+- lib/bel_parser/language/version1_0/relationships/has_modification.rb
+- lib/bel_parser/language/version1_0/relationships/has_product.rb
+- lib/bel_parser/language/version1_0/relationships/has_variant.rb
+- lib/bel_parser/language/version1_0/relationships/includes.rb
+- lib/bel_parser/language/version1_0/relationships/increases.rb
+- lib/bel_parser/language/version1_0/relationships/is_a.rb
+- lib/bel_parser/language/version1_0/relationships/negative_correlation.rb
+- lib/bel_parser/language/version1_0/relationships/orthologous.rb
+- lib/bel_parser/language/version1_0/relationships/positive_correlation.rb
+- lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb
+- lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb
+- lib/bel_parser/language/version1_0/relationships/reactant_in.rb
+- lib/bel_parser/language/version1_0/relationships/sub_process_of.rb
+- lib/bel_parser/language/version1_0/relationships/transcribed_to.rb
+- lib/bel_parser/language/version1_0/relationships/translated_to.rb
+- lib/bel_parser/language/version1_0/relationships/translocates.rb
+- lib/bel_parser/language/version1_0/return_types/abundance.rb
+- lib/bel_parser/language/version1_0/return_types/any.rb
+- lib/bel_parser/language/version1_0/return_types/biological_process.rb
+- lib/bel_parser/language/version1_0/return_types/catalytic_activity.rb
+- lib/bel_parser/language/version1_0/return_types/chaperone_activity.rb
+- lib/bel_parser/language/version1_0/return_types/complex_abundance.rb
+- lib/bel_parser/language/version1_0/return_types/fusion.rb
+- lib/bel_parser/language/version1_0/return_types/gene_abundance.rb
+- lib/bel_parser/language/version1_0/return_types/gtp_bound_activity.rb
+- lib/bel_parser/language/version1_0/return_types/kinase_activity.rb
+- lib/bel_parser/language/version1_0/return_types/list.rb
+- lib/bel_parser/language/version1_0/return_types/micro_rna_abundance.rb
+- lib/bel_parser/language/version1_0/return_types/molecular_activity.rb
+- lib/bel_parser/language/version1_0/return_types/pathology.rb
+- lib/bel_parser/language/version1_0/return_types/peptidase_activity.rb
+- lib/bel_parser/language/version1_0/return_types/phosphatase_activity.rb
+- lib/bel_parser/language/version1_0/return_types/products.rb
+- lib/bel_parser/language/version1_0/return_types/protein_abundance.rb
+- lib/bel_parser/language/version1_0/return_types/protein_modification.rb
+- lib/bel_parser/language/version1_0/return_types/reactants.rb
+- lib/bel_parser/language/version1_0/return_types/ribosylation_activity.rb
+- lib/bel_parser/language/version1_0/return_types/rna_abundance.rb
+- lib/bel_parser/language/version1_0/return_types/substitution.rb
+- lib/bel_parser/language/version1_0/return_types/transcriptional_activity.rb
+- lib/bel_parser/language/version1_0/return_types/transport_activity.rb
+- lib/bel_parser/language/version1_0/return_types/truncation.rb
+- lib/bel_parser/language/version1_0/value_encodings/abundance.rb
+- lib/bel_parser/language/version1_0/value_encodings/any.rb
+- lib/bel_parser/language/version1_0/value_encodings/biological_process.rb
+- lib/bel_parser/language/version1_0/value_encodings/complex_abundance.rb
+- lib/bel_parser/language/version1_0/value_encodings/gene_abundance.rb
+- lib/bel_parser/language/version1_0/value_encodings/micro_rna_abundance.rb
+- lib/bel_parser/language/version1_0/value_encodings/pathology.rb
+- lib/bel_parser/language/version1_0/value_encodings/protein_abundance.rb
+- lib/bel_parser/language/version1_0/value_encodings/rna_abundance.rb
+- lib/bel_parser/language/version2_0.rb
+- lib/bel_parser/language/version2_0/functions/abundance.rb
+- lib/bel_parser/language/version2_0/functions/activity.rb
+- lib/bel_parser/language/version2_0/functions/biological_process.rb
+- lib/bel_parser/language/version2_0/functions/cell_secretion.rb
+- lib/bel_parser/language/version2_0/functions/cell_surface_expression.rb
+- lib/bel_parser/language/version2_0/functions/complex_abundance.rb
+- lib/bel_parser/language/version2_0/functions/composite_abundance.rb
+- lib/bel_parser/language/version2_0/functions/degradation.rb
+- lib/bel_parser/language/version2_0/functions/fragment.rb
+- lib/bel_parser/language/version2_0/functions/from_location.rb
+- lib/bel_parser/language/version2_0/functions/fusion.rb
+- lib/bel_parser/language/version2_0/functions/gene_abundance.rb
+- lib/bel_parser/language/version2_0/functions/list.rb
+- lib/bel_parser/language/version2_0/functions/location.rb
+- lib/bel_parser/language/version2_0/functions/micro_rna_abundance.rb
+- lib/bel_parser/language/version2_0/functions/molecular_activity.rb
+- lib/bel_parser/language/version2_0/functions/pathology.rb
+- lib/bel_parser/language/version2_0/functions/products.rb
+- lib/bel_parser/language/version2_0/functions/protein_abundance.rb
+- lib/bel_parser/language/version2_0/functions/protein_modification.rb
+- lib/bel_parser/language/version2_0/functions/reactants.rb
+- lib/bel_parser/language/version2_0/functions/reaction.rb
+- lib/bel_parser/language/version2_0/functions/rna_abundance.rb
+- lib/bel_parser/language/version2_0/functions/to_location.rb
+- lib/bel_parser/language/version2_0/functions/translocation.rb
+- lib/bel_parser/language/version2_0/functions/variant.rb
+- lib/bel_parser/language/version2_0/relationships/acts_in.rb
+- lib/bel_parser/language/version2_0/relationships/analogous.rb
+- lib/bel_parser/language/version2_0/relationships/association.rb
+- lib/bel_parser/language/version2_0/relationships/biomarker_for.rb
+- lib/bel_parser/language/version2_0/relationships/causes_no_change.rb
+- lib/bel_parser/language/version2_0/relationships/decreases.rb
+- lib/bel_parser/language/version2_0/relationships/directly_decreases.rb
+- lib/bel_parser/language/version2_0/relationships/directly_increases.rb
+- lib/bel_parser/language/version2_0/relationships/has_component.rb
+- lib/bel_parser/language/version2_0/relationships/has_components.rb
+- lib/bel_parser/language/version2_0/relationships/has_member.rb
+- lib/bel_parser/language/version2_0/relationships/has_members.rb
+- lib/bel_parser/language/version2_0/relationships/has_modification.rb
+- lib/bel_parser/language/version2_0/relationships/has_product.rb
+- lib/bel_parser/language/version2_0/relationships/has_variant.rb
+- lib/bel_parser/language/version2_0/relationships/includes.rb
+- lib/bel_parser/language/version2_0/relationships/increases.rb
+- lib/bel_parser/language/version2_0/relationships/is_a.rb
+- lib/bel_parser/language/version2_0/relationships/negative_correlation.rb
+- lib/bel_parser/language/version2_0/relationships/orthologous.rb
+- lib/bel_parser/language/version2_0/relationships/positive_correlation.rb
+- lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb
+- lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb
+- lib/bel_parser/language/version2_0/relationships/reactant_in.rb
+- lib/bel_parser/language/version2_0/relationships/regulates.rb
+- lib/bel_parser/language/version2_0/relationships/sub_process_of.rb
+- lib/bel_parser/language/version2_0/relationships/transcribed_to.rb
+- lib/bel_parser/language/version2_0/relationships/translated_to.rb
+- lib/bel_parser/language/version2_0/relationships/translocates.rb
+- lib/bel_parser/language/version2_0/return_types/abundance.rb
+- lib/bel_parser/language/version2_0/return_types/activity.rb
+- lib/bel_parser/language/version2_0/return_types/any.rb
+- lib/bel_parser/language/version2_0/return_types/biological_process.rb
+- lib/bel_parser/language/version2_0/return_types/complex_abundance.rb
+- lib/bel_parser/language/version2_0/return_types/fragment.rb
+- lib/bel_parser/language/version2_0/return_types/from_location.rb
+- lib/bel_parser/language/version2_0/return_types/fusion.rb
+- lib/bel_parser/language/version2_0/return_types/gene_abundance.rb
+- lib/bel_parser/language/version2_0/return_types/list.rb
+- lib/bel_parser/language/version2_0/return_types/location.rb
+- lib/bel_parser/language/version2_0/return_types/micro_rna_abundance.rb
+- lib/bel_parser/language/version2_0/return_types/molecular_activity.rb
+- lib/bel_parser/language/version2_0/return_types/pathology.rb
+- lib/bel_parser/language/version2_0/return_types/products.rb
+- lib/bel_parser/language/version2_0/return_types/protein_abundance.rb
+- lib/bel_parser/language/version2_0/return_types/protein_modification.rb
+- lib/bel_parser/language/version2_0/return_types/reactants.rb
+- lib/bel_parser/language/version2_0/return_types/rna_abundance.rb
+- lib/bel_parser/language/version2_0/return_types/to_location.rb
+- lib/bel_parser/language/version2_0/return_types/variant.rb
+- lib/bel_parser/language/version2_0/value_encodings/abundance.rb
+- lib/bel_parser/language/version2_0/value_encodings/activity.rb
+- lib/bel_parser/language/version2_0/value_encodings/any.rb
+- lib/bel_parser/language/version2_0/value_encodings/biological_process.rb
+- lib/bel_parser/language/version2_0/value_encodings/complex_abundance.rb
+- lib/bel_parser/language/version2_0/value_encodings/gene_abundance.rb
+- lib/bel_parser/language/version2_0/value_encodings/location.rb
+- lib/bel_parser/language/version2_0/value_encodings/micro_rna_abundance.rb
+- lib/bel_parser/language/version2_0/value_encodings/pathology.rb
+- lib/bel_parser/language/version2_0/value_encodings/protein_abundance.rb
+- lib/bel_parser/language/version2_0/value_encodings/protein_modification.rb
+- lib/bel_parser/language/version2_0/value_encodings/rna_abundance.rb
+- lib/bel_parser/mixin/line_continuator.rb
+- lib/bel_parser/mixin/line_mapping.rb
+- lib/bel_parser/parsers/ast/node.rb
+- lib/bel_parser/parsers/ast/sexp.rb
+- lib/bel_parser/parsers/bel_script.rb
+- lib/bel_parser/parsers/bel_script/define_annotation.rb
+- lib/bel_parser/parsers/bel_script/define_annotation.rl
+- lib/bel_parser/parsers/bel_script/define_namespace.rb
+- lib/bel_parser/parsers/bel_script/define_namespace.rl
+- lib/bel_parser/parsers/bel_script/set.rb
+- lib/bel_parser/parsers/bel_script/set.rl
+- lib/bel_parser/parsers/bel_script/set_document.rb
+- lib/bel_parser/parsers/bel_script/set_document.rl
+- lib/bel_parser/parsers/bel_script/unset.rb
+- lib/bel_parser/parsers/bel_script/unset.rl
+- lib/bel_parser/parsers/common.rb
+- lib/bel_parser/parsers/common/blank_line.rb
+- lib/bel_parser/parsers/common/blank_line.rl
+- lib/bel_parser/parsers/common/comment_line.rb
+- lib/bel_parser/parsers/common/comment_line.rl
+- lib/bel_parser/parsers/common/common.rb
+- lib/bel_parser/parsers/common/common.rl
+- lib/bel_parser/parsers/common/identifier.rb
+- lib/bel_parser/parsers/common/identifier.rl
+- lib/bel_parser/parsers/common/list.rb
+- lib/bel_parser/parsers/common/list.rl
+- lib/bel_parser/parsers/common/string.rb
+- lib/bel_parser/parsers/common/string.rl
+- lib/bel_parser/parsers/expression.rb
+- lib/bel_parser/parsers/expression/comment.rb
+- lib/bel_parser/parsers/expression/comment.rl
+- lib/bel_parser/parsers/expression/nested_statement.rb
+- lib/bel_parser/parsers/expression/nested_statement.rl
+- lib/bel_parser/parsers/expression/observed_term.rb
+- lib/bel_parser/parsers/expression/observed_term.rl
+- lib/bel_parser/parsers/expression/parameter.rb
+- lib/bel_parser/parsers/expression/parameter.rl
+- lib/bel_parser/parsers/expression/relationship.rb
+- lib/bel_parser/parsers/expression/relationship.rl
+- lib/bel_parser/parsers/expression/simple_statement.rb
+- lib/bel_parser/parsers/expression/simple_statement.rl
+- lib/bel_parser/parsers/expression/term.rb
+- lib/bel_parser/parsers/expression/term.rl
+- lib/bel_parser/parsers/line_parser.rb
+- lib/bel_parser/parsers/mixin/buffer.rb
+- lib/bel_parser/parsers/nonblocking_io_wrapper.rb
+- lib/bel_parser/parsers/serializer.rb
+- lib/bel_parser/quoting.rb
+- lib/bel_parser/resource/concept.rb
+- lib/bel_parser/resource/concept_scheme.rb
+- lib/bel_parser/resource/dataset.rb
+- lib/bel_parser/resource/eager_reader.rb
+- lib/bel_parser/resource/eager_sparql_reader.rb
+- lib/bel_parser/resource/file_resource.rb
+- lib/bel_parser/resource/file_resource_value.rb
+- lib/bel_parser/resource/jena_tdb_reader.rb
+- lib/bel_parser/resource/lru_cache.rb
+- lib/bel_parser/resource/lru_reader.rb
+- lib/bel_parser/resource/reader.rb
+- lib/bel_parser/resource/resource_url_reader.rb
+- lib/bel_parser/resource/sparql_reader.rb
+- lib/bel_parser/resource/value.rb
+- lib/bel_parser/script.rb
+- lib/bel_parser/script/filter.rb
+- lib/bel_parser/script/first_node.rb
+- lib/bel_parser/script/keywords.rb
+- lib/bel_parser/script/nanopub_mapper.rb
+- lib/bel_parser/script/parser.rb
+- lib/bel_parser/script/state/annotation_definition.rb
+- lib/bel_parser/script/state/bel_version.rb
+- lib/bel_parser/script/state/document_property.rb
+- lib/bel_parser/script/state/namespace_definition.rb
+- lib/bel_parser/script/state/set.rb
+- lib/bel_parser/script/state/unset.rb
+- lib/bel_parser/script/state_aggregator.rb
+- lib/bel_parser/script/state_function.rb
+- lib/bel_parser/script/syntax/expression_validation.rb
+- lib/bel_parser/script/syntax/invalid_regex_pattern.rb
+- lib/bel_parser/script/syntax/undefined_annotation.rb
+- lib/bel_parser/script/syntax/undefined_annotation_value.rb
+- lib/bel_parser/script/syntax/unresolvable_namespace.rb
+- lib/bel_parser/script/syntax/unsupported_bel_version.rb
+- lib/bel_parser/script/validator.rb
+- lib/bel_parser/vendor/ast.rb
+- lib/bel_parser/vendor/ast/node.rb
+- lib/bel_parser/vendor/ast/processor.rb
+- lib/bel_parser/vendor/ast/processor/mixin.rb
+- lib/bel_parser/vendor/ast/sexp.rb
+homepage: https://github.com/OpenBEL/bel_parser
+licenses:
+- Apache-2.0
+metadata: {}
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.0.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">"
+    - !ruby/object:Gem::Version
+      version: 1.3.1
+requirements: []
+rubyforge_project:
+rubygems_version: 2.6.4
+signing_key:
+specification_version: 4
+summary: Parser for Biolgical Expression Language.
+test_files: []