bel_parser 1.0.0.alpha.1

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

@@ -0,0 +1,12 @@
+module AST
+  # This class includes {AST::Processor::Mixin}; however, it is
+  # deprecated, since the module defines all of the behaviors that
+  # the processor includes.  Any new libraries should use
+  # {AST::Processor::Mixin} instead of subclassing this.
+  #
+  # @deprecated Use {AST::Processor::Mixin} instead.
+  class Processor
+    require_relative 'processor/mixin'
+    include Mixin
+  end
+end

data/lib/bel_parser/vendor/ast/processor/mixin.rb

@@ -0,0 +1,282 @@
+module AST
+  class Processor
+    # The processor module is a module which helps transforming one
+    # AST into another.  In a nutshell, the {#process} method accepts
+    # a {Node} and dispatches it to a handler corresponding to its
+    # type, and returns a (possibly) updated variant of the node.
+    #
+    # The processor module has a set of associated design patterns.
+    # They are best explained with a concrete example. Let's define a
+    # simple arithmetic language and an AST format for it:
+    #
+    # Terminals (AST nodes which do not have other AST nodes inside):
+    #
+    #   * `(integer <int-literal>)`,
+    #
+    # Nonterminals (AST nodes with other nodes as children):
+    #
+    #   * `(add <node> <node>)`,
+    #   * `(multiply <node> <node>)`,
+    #   * `(divide <node> <node>)`,
+    #   * `(negate <node>)`,
+    #   * `(store <node> <string-literal>)`: stores value of `<node>`
+    #     into a variable named `<string-literal>`,
+    #   * `(load <string-literal>)`: loads value of a variable named
+    #     `<string-literal>`,
+    #   * `(each <node> ...): computes each of the `<node>`s and
+    #     prints the result.
+    #
+    # All AST nodes have the same Ruby class, and therefore they don't
+    # know how to traverse themselves. (A solution which dynamically
+    # checks the type of children is possible, but is slow and
+    # error-prone.) So, a class including the module which knows how
+    # to traverse the entire tree should be defined.  Such classes
+    # have a handler for each nonterminal node which recursively
+    # processes children nodes:
+    #
+    #     require 'ast'
+    #
+    #     class ArithmeticsProcessor
+    #       include AST::Processor::Module
+    #       # This method traverses any binary operators such as (add)
+    #       # or (multiply).
+    #       def process_binary_op(node)
+    #         # Children aren't decomposed automatically; it is
+    #         # suggested to use Ruby multiple assignment expansion,
+    #         # as it is very convenient here.
+    #         left_expr, right_expr = *node
+    #
+    #         # AST::Node#updated won't change node type if nil is
+    #         # passed as a first argument, which allows to reuse the
+    #         # same handler for multiple node types using `alias'
+    #         # (below).
+    #         node.updated(nil, [
+    #           process(left_expr),
+    #           process(right_expr)
+    #         ])
+    #       end
+    #       alias_method :on_add,      :process_binary_op
+    #       alias_method :on_multiply, :process_binary_op
+    #       alias_method :on_divide,   :process_binary_op
+    #
+    #       def on_negate(node)
+    #         # It is also possible to use #process_all for more
+    #         # compact code if every child is a Node.
+    #         node.updated(nil, process_all(node))
+    #       end
+    #
+    #       def on_store(node)
+    #         expr, variable_name = *node
+    #
+    #         # Note that variable_name is not a Node and thus isn't
+    #         # passed to #process.
+    #         node.updated(nil, [
+    #           process(expr),
+    #           variable_name
+    #         ])
+    #       end
+    #
+    #       # (load) is effectively a terminal node, and so it does
+    #       # not need an explicit handler, as the following is the
+    #       # default behavior.  Essentially, for any nodes that don't
+    #       # have a defined handler, the node remains unchanged.
+    #       def on_load(node)
+    #         nil
+    #       end
+    #
+    #       def on_each(node)
+    #         node.updated(nil, process_all(node))
+    #       end
+    #     end
+    #
+    # Let's test our ArithmeticsProcessor:
+    #
+    #     include AST::Sexp
+    #     expr = s(:add, s(:integer, 2), s(:integer, 2))
+    #
+    #     p ArithmeticsProcessor.new.process(expr) == expr # => true
+    #
+    # As expected, it does not change anything at all. This isn't
+    # actually very useful, so let's now define a Calculator, which
+    # will compute the expression values:
+    #
+    #     # This Processor folds nonterminal nodes and returns an
+    #     # (integer) terminal node.
+    #     class ArithmeticsCalculator < ArithmeticsProcessor
+    #       def compute_op(node)
+    #         # First, node children are processed and then unpacked
+    #         # to local variables.
+    #         nodes = process_all(node)
+    #
+    #         if nodes.all? { |node| node.type == :integer }
+    #           # If each of those nodes represents a literal, we can
+    #           # fold this node!
+    #           values = nodes.map { |node| node.children.first }
+    #           AST::Node.new(:integer, [
+    #             yield(values)
+    #           ])
+    #         else
+    #           # Otherwise, we can just leave the current node in the
+    #           # tree and only update it with processed children
+    #           # nodes, which can be partially folded.
+    #           node.updated(nil, nodes)
+    #         end
+    #       end
+    #
+    #       def on_add(node)
+    #         compute_op(node) { |left, right| left + right }
+    #       end
+    #
+    #       def on_multiply(node)
+    #         compute_op(node) { |left, right| left * right }
+    #       end
+    #     end
+    #
+    # Let's check:
+    #
+    #     p ArithmeticsCalculator.new.process(expr) # => (integer 4)
+    #
+    # Excellent, the calculator works! Now, a careful reader could
+    # notice that the ArithmeticsCalculator does not know how to
+    # divide numbers. What if we pass an expression with division to
+    # it?
+    #
+    #     expr_with_division = \
+    #       s(:add,
+    #         s(:integer, 1),
+    #         s(:divide,
+    #           s(:add, s(:integer, 8), s(:integer, 4)),
+    #           s(:integer, 3))) # 1 + (8 + 4) / 3
+    #
+    #     folded_expr_with_division = ArithmeticsCalculator.new.process(expr_with_division)
+    #     p folded_expr_with_division
+    #     # => (add
+    #     #      (integer 1)
+    #     #      (divide
+    #     #        (integer 12)
+    #     #        (integer 3)))
+    #
+    # As you can see, the expression was folded _partially_: the inner
+    # `(add)` node which could be computed was folded to
+    # `(integer 12)`, the `(divide)` node is left as-is because there
+    # is no computing handler for it, and the root `(add)` node was
+    # also left as it is because some of its children were not
+    # literals.
+    #
+    # Note that this partial folding is only possible because the
+    # _data_ format, i.e. the format in which the computed values of
+    # the nodes are represented, is the same as the AST itself.  # # Let's extend our ArithmeticsCalculator class further.  # #     class ArithmeticsCalculator #       def on_divide(node) #         compute_op(node) { |left, right| left / right }
+    #       end
+    #
+    #       def on_negate(node)
+    #         # Note how #compute_op works regardless of the operator
+    #         # arity.
+    #         compute_op(node) { |value| -value }
+    #       end
+    #     end
+    #
+    # Now, let's apply our renewed ArithmeticsCalculator to a partial
+    # result of previous evaluation:
+    #
+    #     p ArithmeticsCalculator.new.process(expr_with_division) # => (integer 5)
+    #
+    # Five! Excellent. This is also pretty much how CRuby 1.8 executed
+    # its programs.
+    #
+    # Now, let's do some automated bug searching. Division by zero is
+    # an error, right? So if we could detect that someone has divided
+    # by zero before the program is even run, that could save some
+    # debugging time.
+    #
+    #     class DivisionByZeroVerifier < ArithmeticsProcessor
+    #       class VerificationFailure < Exception; end
+    #
+    #       def on_divide(node)
+    #         # You need to process the children to handle nested divisions
+    #         # such as:
+    #         # (divide
+    #         #   (integer 1)
+    #         #   (divide (integer 1) (integer 0))
+    #         left, right = process_all(node)
+    #
+    #         if right.type == :integer &&
+    #            right.children.first == 0
+    #           raise VerificationFailure, "Ouch! This code divides by zero."
+    #         end
+    #       end
+    #
+    #       def divides_by_zero?(ast)
+    #         process(ast)
+    #         false
+    #       rescue VerificationFailure
+    #         true
+    #       end
+    #     end
+    #
+    #     nice_expr = \
+    #       s(:divide,
+    #         s(:add, s(:integer, 10), s(:integer, 2)),
+    #         s(:integer, 4))
+    #
+    #     p DivisionByZeroVerifier.new.divides_by_zero?(nice_expr)
+    #     # => false. Good.
+    #
+    #     bad_expr = \
+    #       s(:add, s(:integer, 10),
+    #         s(:divide, s(:integer, 1), s(:integer, 0)))
+    #
+    #     p DivisionByZeroVerifier.new.divides_by_zero?(bad_expr)
+    #     # => true. WHOOPS. DO NOT RUN THIS.
+    #
+    # Of course, this won't detect more complex cases... unless you
+    # use some partial evaluation before! The possibilites are
+    # endless. Have fun.
+    module Mixin
+      # Dispatches `node`. If a node has type `:foo`, then a handler
+      # named `on_foo` is invoked with one argument, the `node`; if
+      # there isn't such a handler, {#handler_missing} is invoked
+      # with the same argument.
+      #
+      # If the handler returns `nil`, `node` is returned; otherwise,
+      # the return value of the handler is passed along.
+      #
+      # @param  [AST::Node, nil] node
+      # @return [AST::Node, nil]
+      def process(node)
+        return if node.nil?
+
+        node = node.to_ast
+
+        # Invoke a specific handler
+        on_handler = :"on_#{node.type}"
+        if respond_to? on_handler
+          new_node = send on_handler, node
+        else
+          new_node = handler_missing(node)
+        end
+
+        node = new_node if new_node
+
+        node
+      end
+
+      # {#process}es each node from `nodes` and returns an array of
+      # results.
+      #
+      # @param  [Array<AST::Node>] nodes
+      # @return [Array<AST::Node>]
+      def process_all(nodes)
+        nodes.to_a.map do |node|
+          process node
+        end
+      end
+
+      # Default handler. Does nothing.
+      #
+      # @param  [AST::Node] node
+      # @return [AST::Node, nil]
+      def handler_missing(node)
+      end
+    end
+  end
+end

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 +1,226 @@
+--- !ruby/object:Gem::Specification
+name: bel_parser
+version: !ruby/object:Gem::Version
+  version: 1.0.0.alpha.1
+platform: ruby
+authors:
+- Anthony Bargnesi
+- Nick Bargnesi
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2016-04-05 00:00:00.000000000 Z
+dependencies: []
+description: Implements language versions 1.0 and 2.0.
+email: abargnesi@selventa.com
+executables:
+- bel2_termcheck
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gemspec"
+- CHANGELOG.md
+- LICENSE
+- README.md
+- VERSION
+- bin/bel2_termcheck
+- lib/bel_parser.rb
+- lib/bel_parser/ast_filter.rb
+- lib/bel_parser/ast_generator.rb
+- lib/bel_parser/ast_validator.rb
+- lib/bel_parser/expression/parser.rb
+- lib/bel_parser/expression/term_semantics.rb
+- lib/bel_parser/language.rb
+- lib/bel_parser/language/function.rb
+- lib/bel_parser/language/quoting.rb
+- lib/bel_parser/language/semantic_ast.rb
+- lib/bel_parser/language/semantics/analyzer.rb
+- lib/bel_parser/language/signature.rb
+- lib/bel_parser/language/specification.rb
+- lib/bel_parser/language/syntax/expression/incomplete_node.rb
+- lib/bel_parser/language/syntax/expression/invalid_term_function.rb
+- lib/bel_parser/language/version1.rb
+- lib/bel_parser/language/version1/functions/abundance.rb
+- lib/bel_parser/language/version1/functions/biological_process.rb
+- lib/bel_parser/language/version1/functions/catalytic_activity.rb
+- lib/bel_parser/language/version1/functions/cell_secretion.rb
+- lib/bel_parser/language/version1/functions/cell_surface_expression.rb
+- lib/bel_parser/language/version1/functions/chaperone_activity.rb
+- lib/bel_parser/language/version1/functions/complex_abundance.rb
+- lib/bel_parser/language/version1/functions/composite_abundance.rb
+- lib/bel_parser/language/version1/functions/degradation.rb
+- lib/bel_parser/language/version1/functions/fusion.rb
+- lib/bel_parser/language/version1/functions/gene_abundance.rb
+- lib/bel_parser/language/version1/functions/gtp_bound_activity.rb
+- lib/bel_parser/language/version1/functions/kinase_activity.rb
+- lib/bel_parser/language/version1/functions/list.rb
+- lib/bel_parser/language/version1/functions/micro_rna_abundance.rb
+- lib/bel_parser/language/version1/functions/molecular_activity.rb
+- lib/bel_parser/language/version1/functions/pathology.rb
+- lib/bel_parser/language/version1/functions/peptidase_activity.rb
+- lib/bel_parser/language/version1/functions/phosphatase_activity.rb
+- lib/bel_parser/language/version1/functions/products.rb
+- lib/bel_parser/language/version1/functions/protein_abundance.rb
+- lib/bel_parser/language/version1/functions/protein_modification.rb
+- lib/bel_parser/language/version1/functions/reactants.rb
+- lib/bel_parser/language/version1/functions/reaction.rb
+- lib/bel_parser/language/version1/functions/ribosylation_activity.rb
+- lib/bel_parser/language/version1/functions/rna_abundance.rb
+- lib/bel_parser/language/version1/functions/substitution.rb
+- lib/bel_parser/language/version1/functions/transcriptional_activity.rb
+- lib/bel_parser/language/version1/functions/translocation.rb
+- lib/bel_parser/language/version1/functions/transport_activity.rb
+- lib/bel_parser/language/version1/functions/truncation.rb
+- lib/bel_parser/language/version1/return_types/abundance.rb
+- lib/bel_parser/language/version1/return_types/any.rb
+- lib/bel_parser/language/version1/return_types/biological_process.rb
+- lib/bel_parser/language/version1/return_types/catalytic_activity.rb
+- lib/bel_parser/language/version1/return_types/chaperone_activity.rb
+- lib/bel_parser/language/version1/return_types/complex_abundance.rb
+- lib/bel_parser/language/version1/return_types/fusion.rb
+- lib/bel_parser/language/version1/return_types/gene_abundance.rb
+- lib/bel_parser/language/version1/return_types/gtp_bound_activity.rb
+- lib/bel_parser/language/version1/return_types/kinase_activity.rb
+- lib/bel_parser/language/version1/return_types/list.rb
+- lib/bel_parser/language/version1/return_types/micro_rna_abundance.rb
+- lib/bel_parser/language/version1/return_types/molecular_activity.rb
+- lib/bel_parser/language/version1/return_types/pathology.rb
+- lib/bel_parser/language/version1/return_types/peptidase_activity.rb
+- lib/bel_parser/language/version1/return_types/phosphatase_activity.rb
+- lib/bel_parser/language/version1/return_types/products.rb
+- lib/bel_parser/language/version1/return_types/protein_abundance.rb
+- lib/bel_parser/language/version1/return_types/protein_modification.rb
+- lib/bel_parser/language/version1/return_types/reactants.rb
+- lib/bel_parser/language/version1/return_types/ribosylation_activity.rb
+- lib/bel_parser/language/version1/return_types/rna_abundance.rb
+- lib/bel_parser/language/version1/return_types/substitution.rb
+- lib/bel_parser/language/version1/return_types/transcriptional_activity.rb
+- lib/bel_parser/language/version1/return_types/transport_activity.rb
+- lib/bel_parser/language/version1/return_types/truncation.rb
+- lib/bel_parser/language/version2.rb
+- lib/bel_parser/language/version2/functions/abundance.rb
+- lib/bel_parser/language/version2/functions/activity.rb
+- lib/bel_parser/language/version2/functions/biological_process.rb
+- lib/bel_parser/language/version2/functions/cell_secretion.rb
+- lib/bel_parser/language/version2/functions/cell_surface_expression.rb
+- lib/bel_parser/language/version2/functions/complex_abundance.rb
+- lib/bel_parser/language/version2/functions/composite_abundance.rb
+- lib/bel_parser/language/version2/functions/degradation.rb
+- lib/bel_parser/language/version2/functions/fragment.rb
+- lib/bel_parser/language/version2/functions/from_location.rb
+- lib/bel_parser/language/version2/functions/fusion.rb
+- lib/bel_parser/language/version2/functions/gene_abundance.rb
+- lib/bel_parser/language/version2/functions/list.rb
+- lib/bel_parser/language/version2/functions/location.rb
+- lib/bel_parser/language/version2/functions/micro_rna_abundance.rb
+- lib/bel_parser/language/version2/functions/molecular_activity.rb
+- lib/bel_parser/language/version2/functions/pathology.rb
+- lib/bel_parser/language/version2/functions/products.rb
+- lib/bel_parser/language/version2/functions/protein_abundance.rb
+- lib/bel_parser/language/version2/functions/protein_modification.rb
+- lib/bel_parser/language/version2/functions/reactants.rb
+- lib/bel_parser/language/version2/functions/reaction.rb
+- lib/bel_parser/language/version2/functions/rna_abundance.rb
+- lib/bel_parser/language/version2/functions/to_location.rb
+- lib/bel_parser/language/version2/functions/translocation.rb
+- lib/bel_parser/language/version2/functions/variant.rb
+- lib/bel_parser/language/version2/return_types/abundance.rb
+- lib/bel_parser/language/version2/return_types/activity.rb
+- lib/bel_parser/language/version2/return_types/any.rb
+- lib/bel_parser/language/version2/return_types/biological_process.rb
+- lib/bel_parser/language/version2/return_types/complex_abundance.rb
+- lib/bel_parser/language/version2/return_types/fragment.rb
+- lib/bel_parser/language/version2/return_types/from_location.rb
+- lib/bel_parser/language/version2/return_types/fusion.rb
+- lib/bel_parser/language/version2/return_types/gene_abundance.rb
+- lib/bel_parser/language/version2/return_types/list.rb
+- lib/bel_parser/language/version2/return_types/location.rb
+- lib/bel_parser/language/version2/return_types/micro_rna_abundance.rb
+- lib/bel_parser/language/version2/return_types/molecular_activity.rb
+- lib/bel_parser/language/version2/return_types/pathology.rb
+- lib/bel_parser/language/version2/return_types/products.rb
+- lib/bel_parser/language/version2/return_types/protein_abundance.rb
+- lib/bel_parser/language/version2/return_types/protein_modification.rb
+- lib/bel_parser/language/version2/return_types/reactants.rb
+- lib/bel_parser/language/version2/return_types/rna_abundance.rb
+- lib/bel_parser/language/version2/return_types/to_location.rb
+- lib/bel_parser/language/version2/return_types/variant.rb
+- lib/bel_parser/mixin/line_continuator.rb
+- lib/bel_parser/mixin/line_mapping.rb
+- lib/bel_parser/parser.rb
+- lib/bel_parser/parsers/ast/mapped_traversal.rb
+- lib/bel_parser/parsers/ast/node.rb
+- lib/bel_parser/parsers/ast/sexp.rb
+- lib/bel_parser/parsers/ast/traversal.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/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/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/statement_nested.rb
+- lib/bel_parser/parsers/expression/statement_nested.rl
+- lib/bel_parser/parsers/expression/statement_observed_term.rb
+- lib/bel_parser/parsers/expression/statement_observed_term.rl
+- lib/bel_parser/parsers/expression/statement_simple.rb
+- lib/bel_parser/parsers/expression/statement_simple.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/script/parser.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: 2.5.1
+signing_key: 
+specification_version: 4
+summary: Parser for Biolgical Expression Language.
+test_files: []
+has_rdoc: