openbel-api 0.4.0-java

data/lib/openbel/api/plugin/plugin.rb

@@ -0,0 +1,99 @@
+module OpenBEL
+  module Plugin
+
+    EMPTY_ARRAY = [].freeze
+
+    INCLUSION_MUTEX = Mutex.new
+    private_constant :INCLUSION_MUTEX
+
+    def self.included(base)
+      INCLUSION_MUTEX.lock
+      begin
+        unless OpenBEL.const_defined?(:PluginClasses)
+          OpenBEL.const_set(:PluginClasses, [])
+        end
+        OpenBEL::PluginClasses << base
+      ensure
+        INCLUSION_MUTEX.unlock
+      end
+    end
+
+    def id
+      fail NotImplementedError.new("#{__method__} not implemented")
+    end
+
+    def name
+      fail NotImplementedError.new("#{__method__} not implemented")
+    end
+
+    def description
+      fail NotImplementedError.new("#{__method__} not implemented")
+    end
+
+    def type
+      fail NotImplementedError.new("#{__method__} not implemented.")
+    end
+
+    def required_extensions
+      []
+    end
+
+    def optional_extensions
+      []
+    end
+
+    def validate(extensions = {}, options = {})
+      validation_successful
+    end
+
+    def on_load; end
+
+    def configure(extensions = {}, options = {}); end
+
+    def create_instance; end
+
+    def on_unload; end
+
+    def <=>(other)
+      id_compare = id.to_s <=> other.to_s
+      return id_compare unless id_compare == 0
+      return self.name.to_s <=> other.name.to_s
+    end
+
+    def hash
+      [id, name].hash
+    end
+
+    def ==(other)
+      return false if other == nil
+      return true if self.equal? other
+      self.id == other.id && self.name == other.name
+    end
+    alias_method :eql?, :'=='
+
+    protected
+
+    def validation_successful
+      EMPTY_ARRAY
+    end
+
+    def mri?
+      defined?(RUBY_DESCRIPTION) && (/^ruby/ =~ RUBY_DESCRIPTION)
+    end
+
+    def jruby?
+      defined?(RUBY_PLATFORM) && ("java" == RUBY_PLATFORM)
+    end
+
+    def rubinius?
+      defined?(RUBY_ENGINE) && ("rbx" == RUBY_ENGINE)
+    end
+
+    ValidationError = Struct.new(:plugin, :field, :error) do
+
+      def to_s
+        "Error with #{field} field of #{plugin.id} (#{plugin.name}): #{error}"
+      end
+    end
+  end
+end

data/lib/openbel/api/plugin/plugin_manager.rb

@@ -0,0 +1,20 @@
+require_relative 'configure_plugins'
+require_relative 'plugin_repository'
+
+module OpenBEL
+
+  class PluginManager
+    include ConfigurePlugins
+    include PluginRepository
+
+    def report_plugins_available
+      map { |plugin|
+        "id: #{plugin.id}
+  name:        #{plugin.name}
+  description: #{plugin.description}
+  class:       #{plugin.class}
+        "
+      }
+    end
+  end
+end

data/lib/openbel/api/plugin/plugin_repository.rb

@@ -0,0 +1,60 @@
+require 'pathname'
+
+module OpenBEL
+  module PluginRepository
+    include Enumerable
+
+    WRITE_MUTEX = Mutex.new
+
+    def with_plugins_from(*paths)
+      WRITE_MUTEX.lock
+      begin
+        (@paths ||= []).concat paths.flatten.compact.uniq
+      ensure
+        WRITE_MUTEX.unlock
+      end
+      self
+    end
+
+    def find_plugins(id, type = nil)
+      find_all { |p|
+        ([p.id, p.name].include? id) and (!type or p.type == type.to_s.to_sym)
+      }
+    end
+
+    def each
+      WRITE_MUTEX.lock
+      begin
+        @paths ||= []
+        if block_given?
+          require_plugins(@paths)
+          plugins.each { |p| yield p.new }
+        else
+          enum_for(:each)
+        end
+      ensure
+        WRITE_MUTEX.unlock
+      end
+    end
+    alias_method :each_plugin, :each
+
+    private
+
+    def plugins
+      OpenBEL::PluginClasses.uniq
+    end
+
+    def require_plugins(paths)
+      [paths].flatten.compact.uniq.each do |p|
+        p << File::SEPARATOR if not p.end_with? File::SEPARATOR
+        Dir["#{p}*.rb"].each do |source|
+          if Pathname.new(source).absolute?
+            require source
+          else
+            require ".#{File::SEPARATOR}#{source}"
+          end
+        end
+      end
+    end
+  end
+end

data/lib/openbel/api/storage/cache_proxy.rb

@@ -0,0 +1,74 @@
+require_relative 'triple_storage'
+
+module OpenBEL
+  module Storage
+    class CacheProxy
+      include TripleStorage
+
+      def initialize(real_storage, cache)
+        if !real_storage or !real_storage.respond_to?(:triples)
+          fail ArgumentError, "real_storage is invalid."
+        end
+        if !cache or !cache.respond_to?(:[])
+          fail ArgumentError, "cache is invalid."
+        end
+        @real_storage = real_storage
+        @cache = cache
+      end
+
+      def triples(subject, predicate, object, options={})
+        pattern_key = key(subject, predicate, object)
+        rdf_value = @cache[pattern_key]
+        map_method = options.delete(:only)
+        if rdf_value
+          return [] if rdf_value == ""
+          triples = unpack(rdf_value).each_slice(3)
+        else
+          triples = @real_storage.triples(subject, predicate, object, options).to_a
+          if triples.empty?
+            @cache[pattern_key] = ""
+          else
+            rdf_value = triples.map { |stmt|
+              [subject(stmt), predicate(stmt), object(stmt)]
+            }.flatten
+            @cache[pattern_key] = pack(rdf_value)
+          end
+          triples
+        end
+
+        map_method = if map_method && @real_storage.respond_to?(map_method)
+                       @real_storage.method(map_method)
+                     else
+                       @real_storage.method(:all)
+                     end
+        if block_given?
+          triples.each { |triple| yield map_method.call(triple) }
+        else
+          triples = triples.respond_to?(:lazy) ? triples.lazy : triples
+          triples.map { |triple| map_method.call(triple) }
+        end
+      end
+
+      private
+
+      def key(subject, predicate, object)
+        pack([
+          subject   == nil ? 'NULL' : subject.to_s,
+          predicate == nil ? 'NULL' : predicate.to_s,
+          object    == nil ? 'NULL' : object.to_s,
+        ])
+      end
+
+      def pack(array)
+        [array.join("\0")].pack('m0')
+      end
+
+      def unpack(value)
+        return nil unless value
+        value.unpack('m*')[0].split("\0")
+      end
+    end
+  end
+end
+# vim: ts=2 sts=2 sw=2 expandtab
+# encoding: utf-8

data/lib/openbel/api/storage/triple_storage.rb

@@ -0,0 +1,43 @@
+module OpenBEL
+  module Storage
+    module TripleStorage
+
+      def triples(subject, predicate, object, options={})
+        fail NotImplementedError, "#{__method__} is not implemented"
+      end
+
+      def all(statement)
+        if statement.respond_to? :subject
+          [
+            statement.subject.to_s[1..-2],
+            statement.predicate.to_s[1..-2],
+            object(statement)
+          ]
+        else
+          statement
+        end
+      end
+
+      def subject(statement)
+        return statement.subject.to_s[1..-2] if statement.respond_to? :subject
+        statement[0]
+      end
+
+      def predicate(statement)
+        return statement.predicate.to_s[1..-2] if statement.respond_to? :predicate
+        statement[1]
+      end
+
+      def object(statement)
+        if statement.respond_to? :object
+          object = statement.object
+          (object.literal? && object.value.to_s) || object.to_s[1..-2]
+        else
+          statement[2]
+        end
+      end
+    end
+  end
+end
+# vim: ts=2 sts=2 sw=2 expandtab
+# encoding: utf-8

metadata

@@ -0,0 +1,379 @@
+--- !ruby/object:Gem::Specification
+name: openbel-api
+version: !ruby/object:Gem::Version
+  version: 0.4.0
+platform: java
+authors:
+- Anthony Bargnesi
+- Nick Bargnesi
+- William Hayes
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2015-12-02 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+  name: bel
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+  name: bel-search-sqlite
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+  name: bel-rdf-jena
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.99.0
+  name: rdf
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.99.0
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.12.5
+  name: mongo
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.12.5
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.12.5
+  name: bson
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.12.5
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.5.9
+  name: dot_hash
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.5.9
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.3.7
+  name: jrjackson
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.3.7
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.10.0
+  name: json_schema
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.10.0
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.11.2
+  name: multi_json
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.11.2
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.4.6
+  name: oat
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.4.6
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 2.15.3
+  name: puma
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 2.15.3
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.6.4
+  name: rack
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.6.4
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+  name: rack-cors
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.7.0
+  name: rack-handlers
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.7.0
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.4.6
+  name: sinatra
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.4.6
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.4.6
+  name: sinatra-contrib
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.4.6
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.5.2
+  name: jwt
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.5.2
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.8.0
+  name: rest-client
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.8.0
+description: The OpenBEL API provides a RESTful API over HTTP to manage BEL knowledge.
+email: abargnesi@selventa.com
+executables:
+- openbel-config
+- openbel-api
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gemspec"
+- CHANGELOG.md
+- INSTALL.md
+- INSTALL_RUBY.md
+- LICENSE
+- README.md
+- app/openbel/api/app.rb
+- app/openbel/api/config.rb
+- app/openbel/api/config.ru
+- app/openbel/api/helpers/pager.rb
+- app/openbel/api/middleware/auth.rb
+- app/openbel/api/resources/adapters/basic_json.rb
+- app/openbel/api/resources/annotation.rb
+- app/openbel/api/resources/base.rb
+- app/openbel/api/resources/completion.rb
+- app/openbel/api/resources/evidence.rb
+- app/openbel/api/resources/evidence_transform.rb
+- app/openbel/api/resources/function.rb
+- app/openbel/api/resources/match_result.rb
+- app/openbel/api/resources/namespace.rb
+- app/openbel/api/routes/annotations.rb
+- app/openbel/api/routes/authenticate.rb
+- app/openbel/api/routes/base.rb
+- app/openbel/api/routes/datasets.rb
+- app/openbel/api/routes/evidence.rb
+- app/openbel/api/routes/expressions.rb
+- app/openbel/api/routes/functions.rb
+- app/openbel/api/routes/namespaces.rb
+- app/openbel/api/routes/root.rb
+- app/openbel/api/schemas.rb
+- app/openbel/api/schemas/annotation_collection.schema.json
+- app/openbel/api/schemas/annotation_resource.schema.json
+- app/openbel/api/schemas/annotation_value_collection.schema.json
+- app/openbel/api/schemas/annotation_value_resource.schema.json
+- app/openbel/api/schemas/completion_collection.schema.json
+- app/openbel/api/schemas/completion_resource.schema.json
+- app/openbel/api/schemas/evidence.schema.json
+- app/openbel/api/schemas/evidence_collection.schema.json
+- app/openbel/api/schemas/evidence_resource.schema.json
+- app/openbel/api/schemas/namespace_value_collection.schema.json
+- app/openbel/api/schemas/namespace_value_resource.schema.json
+- app/openbel/api/util.rb
+- bin/openbel-api
+- bin/openbel-config
+- config/async_evidence.rb
+- config/async_jena.rb
+- config/config.yml
+- config/server_config.rb
+- lib/openbel/api/cache/cache.rb
+- lib/openbel/api/config/config.rb
+- lib/openbel/api/evidence/api.rb
+- lib/openbel/api/evidence/facet_api.rb
+- lib/openbel/api/evidence/facet_filter.rb
+- lib/openbel/api/evidence/mongo.rb
+- lib/openbel/api/evidence/mongo_facet.rb
+- lib/openbel/api/helpers/dependency_graph.rb
+- lib/openbel/api/model/rdf_resource.rb
+- lib/openbel/api/plugin/cache/kyotocabinet.rb
+- lib/openbel/api/plugin/configure_plugins.rb
+- lib/openbel/api/plugin/evidence/evidence.rb
+- lib/openbel/api/plugin/plugin.rb
+- lib/openbel/api/plugin/plugin_manager.rb
+- lib/openbel/api/plugin/plugin_repository.rb
+- lib/openbel/api/storage/cache_proxy.rb
+- lib/openbel/api/storage/triple_storage.rb
+homepage: https://github.com/OpenBEL/openbel-server
+licenses:
+- Apache-2.0
+metadata: {}
+post_install_message:
+rdoc_options: []
+require_paths:
+- app
+- 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: '0'
+requirements: []
+rubyforge_project:
+rubygems_version: 2.4.8
+signing_key:
+specification_version: 4
+summary: The OpenBEL API provided over RESTful HTTP endpoints.
+test_files: []