openbel-api 0.6.2-java → 1.0.0-java

data/lib/openbel/api/{evidence → nanopub}/mongo_facet.rb

@@ -2,14 +2,16 @@ require 'mongo'
 require 'multi_json'
 require_relative 'facet_api'
 require_relative 'facet_filter'
+require_relative '../helpers/uuid_generator'
 
 module OpenBEL
-  module Evidence
+  module Nanopub
 
-    class EvidenceFacets
+    class NanopubFacets
       include FacetAPI
       include Mongo
       include FacetFilter
+      include ::OpenBEL::Helpers::UUIDGenerator
 
       def initialize(options = {})
         host = options[:host]
@@ -30,8 +32,8 @@ module OpenBEL
           @db.authenticate(username, password, nil, auth_db)
         end
 
-        @evidence             = @db[:evidence]
-        @evidence_facet_cache = @db[:evidence_facet_cache]
+        @nanopub             = @db[:nanopub]
+        @nanopub_facet_cache = @db[:nanopub_facet_cache]
 
         # ensure all indexes are created and maintained
         ensure_all_indexes
@@ -42,10 +44,10 @@ module OpenBEL
         cache_collection = facet_cache_collection(sorted_filters)
 
         if no_collection?(cache_collection)
-          cache_collection = "evidence_facet_cache_#{EvidenceFacets.generate_uuid}"
+          cache_collection = "nanopub_facet_cache_#{generate_uuid}"
           create_aggr      = create_aggregation(cache_collection, query)
-          @evidence.aggregate(create_aggr[:pipeline], create_aggr[:options])
-          @evidence_facet_cache.insert({
+          @nanopub.aggregate(create_aggr[:pipeline], create_aggr[:options])
+          @nanopub_facet_cache.insert({
             :filters          => sorted_filters,
             :cache_collection => cache_collection
           })
@@ -82,7 +84,7 @@ module OpenBEL
         facets.unshift([])
 
         # Drop facet cache collections
-        @evidence_facet_cache.find(
+        @nanopub_facet_cache.find(
           {:filters => {:$in => facets}},
           :fields => {:_id => 0, :cache_collection => 1}
         ).each do |doc|
@@ -90,12 +92,12 @@ module OpenBEL
           @db[cache_collection].drop()
         end
 
-        # remove filter match entries in evidence_facet_cache
-        @evidence_facet_cache.remove({:filters => {:$in => facets}})
+        # remove filter match entries in nanopub_facet_cache
+        @nanopub_facet_cache.remove({:filters => {:$in => facets}})
       end
 
       def delete_all_facets
-        @evidence_facet_cache.find(
+        @nanopub_facet_cache.find(
           {},
           :fields => {:_id => 0, :cache_collection => 1}
         ).each do |doc|
@@ -103,12 +105,12 @@ module OpenBEL
           @db[cache_collection].drop()
         end
 
-        # remove all entries in evidence_facet_cache
-        @evidence_facet_cache.remove({})
+        # remove all entries in nanopub_facet_cache
+        @nanopub_facet_cache.remove({})
       end
 
       def ensure_all_indexes
-        @evidence_facet_cache.ensure_index([
+        @nanopub_facet_cache.ensure_index([
             [:"filters.category",   Mongo::ASCENDING],
             [:"filters.name",       Mongo::ASCENDING]
           ],
@@ -132,7 +134,7 @@ module OpenBEL
       end
 
       def facet_cache_collection(filters)
-        result = @evidence_facet_cache.find_one(
+        result = @nanopub_facet_cache.find_one(
           {:filters => filters},
           :fields => {:cache_collection => 1, :_id => 0}
         )
@@ -203,19 +205,6 @@ module OpenBEL
           :allowDiskUse => true
         }
       }
-
-      # Define UUID implementation based on Ruby.
-      if RUBY_ENGINE =~ /^jruby/i
-        java_import 'java.util.UUID'
-        define_singleton_method(:generate_uuid) do
-          Java::JavaUtil::UUID.random_uuid.to_s
-        end
-      else
-        require 'uuid'
-        define_singleton_method(:generate_uuid) do
-          UUID.generate
-        end
-      end
     end
   end
 end

data/lib/openbel/api/plugin/{evidence/evidence.rb → nanopub/nanopub.rb}

@@ -3,12 +3,12 @@ require_relative '../plugin'
 module OpenBEL
   module Plugin
 
-    class Evidence
+    class Nanopub
       include OpenBEL::Plugin
 
-      ID = 'evidence'
-      NAME = 'OpenBEL Evidence API'
-      DESC = 'API for accesing OpenBEL Evidence.'
+      ID = 'nanopub'
+      NAME = 'OpenBEL Nanopub API'
+      DESC = 'API for accesing OpenBEL Nanopub.'
 
       def id
         ID
@@ -23,7 +23,7 @@ module OpenBEL
       end
 
       def type
-        :evidence
+        :nanopub
       end
 
       def required_extensions
@@ -35,7 +35,7 @@ module OpenBEL
       end
 
       def on_load
-        require_relative '../../evidence/mongo'
+        require_relative '../../nanopub/mongo'
       end
 
       def validate(extensions = {}, options = {})
@@ -51,7 +51,7 @@ module OpenBEL
       end
 
       def create_instance
-        OpenBEL::Evidence::Evidence.new(@options)
+        OpenBEL::Nanopub::Nanopub.new(@options)
       end
     end
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: openbel-api
 version: !ruby/object:Gem::Version
-  version: 0.6.2
+  version: 1.0.0
 platform: java
 authors:
 - Anthony Bargnesi
@@ -15,23 +15,23 @@ dependencies:
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.6.0
+        version: 1.0.0
   name: bel
   prerelease: false
   type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.6.0
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 1.99.0
+        version: 2.0.0
   name: json-ld
   prerelease: false
   type: :runtime
@@ -39,13 +39,13 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 1.99.0
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 1.99.0
+        version: 2.0.0
   name: rdf-json
   prerelease: false
   type: :runtime
@@ -53,13 +53,13 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 1.99.0
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 1.99.0
+        version: 2.0.0
   name: rdf-rdfa
   prerelease: false
   type: :runtime
@@ -67,13 +67,13 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 1.99.0
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 1.99.0
+        version: 2.0.0
   name: rdf-rdfxml
   prerelease: false
   type: :runtime
@@ -81,13 +81,13 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 1.99.0
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 1.99.0.1
+        version: 2.0.0
   name: rdf-trig
   prerelease: false
   type: :runtime
@@ -95,13 +95,13 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 1.99.0.1
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 1.99.0
+        version: 2.0.0
   name: rdf-trix
   prerelease: false
   type: :runtime
@@ -109,13 +109,13 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 1.99.0
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 1.99.0
+        version: 2.0.0
   name: rdf-turtle
   prerelease: false
   type: :runtime
@@ -123,49 +123,35 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 1.99.0
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.4.2
+        version: 1.0.0.beta
   name: bel-search-sqlite
   prerelease: false
   type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.4.2
+        version: 1.0.0.beta
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.4.2
+        version: 1.0.0.beta
   name: bel-rdf-jena
   prerelease: false
   type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 0.4.2
-- !ruby/object:Gem::Dependency
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 1.99.1
-  name: rdf
-  prerelease: false
-  type: :runtime
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - '='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.99.1
+        version: 1.0.0.beta
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
@@ -381,8 +367,8 @@ files:
 - app/openbel/api/config.rb
 - app/openbel/api/config.ru
 - app/openbel/api/helpers/base.rb
-- app/openbel/api/helpers/evidence.rb
 - app/openbel/api/helpers/filters.rb
+- app/openbel/api/helpers/nanopub.rb
 - app/openbel/api/helpers/pager.rb
 - app/openbel/api/helpers/translators.rb
 - app/openbel/api/middleware/auth.rb
@@ -390,19 +376,20 @@ files:
 - 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/resources/nanopub.rb
+- app/openbel/api/resources/nanopub_transform.rb
+- app/openbel/api/resources/relationship.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/language.rb
 - app/openbel/api/routes/namespaces.rb
+- app/openbel/api/routes/nanopubs.rb
 - app/openbel/api/routes/root.rb
 - app/openbel/api/routes/version.rb
 - app/openbel/api/schemas.rb
@@ -412,11 +399,11 @@ files:
 - 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/schemas/nanopub.schema.json
+- app/openbel/api/schemas/nanopub_collection.schema.json
+- app/openbel/api/schemas/nanopub_resource.schema.json
 - app/openbel/api/util.rb
 - app/openbel/api/version.rb
 - bin/openbel-api
@@ -425,16 +412,17 @@ files:
 - 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/helpers/uuid_generator.rb
 - lib/openbel/api/model/rdf_resource.rb
+- lib/openbel/api/nanopub/api.rb
+- lib/openbel/api/nanopub/facet_api.rb
+- lib/openbel/api/nanopub/facet_filter.rb
+- lib/openbel/api/nanopub/mongo.rb
+- lib/openbel/api/nanopub/mongo_facet.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/nanopub/nanopub.rb
 - lib/openbel/api/plugin/plugin.rb
 - lib/openbel/api/plugin/plugin_manager.rb
 - lib/openbel/api/plugin/plugin_repository.rb
@@ -461,7 +449,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project:
-rubygems_version: 2.4.8
+rubygems_version: 2.6.4
 signing_key:
 specification_version: 4
 summary: The OpenBEL API provided over RESTful HTTP endpoints.

data/app/openbel/api/routes/functions.rb

@@ -1,41 +0,0 @@
-require 'bel'
-
-module OpenBEL
-  module Routes
-
-    class Functions < Base
-      include BEL::Language
-
-      SORTED_FUNCTIONS = FUNCTIONS.values.uniq.sort_by { |fx|
-        fx[:short_form]
-      }
-
-      options '/api/functions' do
-        response.headers['Allow'] = 'OPTIONS,GET'
-        status 200
-      end
-
-      options '/api/functions/:fx' do
-        response.headers['Allow'] = 'OPTIONS,GET'
-        status 200
-      end
-
-      get '/api/functions' do
-        render(SORTED_FUNCTIONS, :function_collection)
-      end
-
-      # BEL Completion
-      get '/api/functions/:fx' do
-        fx_match = FUNCTIONS[params[:fx].to_sym]
-        halt 404 unless fx_match
-
-        render(
-          [fx_match],
-          :function_collection
-        )
-      end
-    end
-  end
-end
-# vim: ts=2 sw=2:
-# encoding: utf-8