openbel-api 1.0.4-java → 1.1.0-java

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 00a36abdeadf9bbfeaf6bd2251e2f7cd32b051bf
-  data.tar.gz: 29e80343fd5d984c9df84266fe707ded3fc10658
+  metadata.gz: 21f37fc7e4b79123c240c3ff5032cf636ce08b2e
+  data.tar.gz: 9e132e96f9542dff268447a45ae9a3d38440239d
 SHA512:
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+  data.tar.gz: 45596461fe4067da77a3307ff48a3ecdca51f492c1d32d50df6e7df105b89d9d708f29e45dea55151d98f0d4fc3eae36004ffaf0feb371cf8cf8e3a7a181d2ce

data/.gemspec

@@ -11,7 +11,7 @@ Gem::Specification.new do |spec|
                                  'Nick Bargnesi',
                                  'William Hayes'
                                ]
-  spec.date                  = %q{2016-03-23}
+  spec.date                  = %q{2017-01-13}
   spec.email                 = %q{abargnesi@selventa.com}
   spec.files                 = [
                                  Dir.glob('app/**/*.{json,rb,ru}'),
@@ -33,24 +33,21 @@ Gem::Specification.new do |spec|
 
   # Dependencies
 
-  ## bel.rb
-  spec.add_runtime_dependency 'bel',               '~> 1.0.0'
+  ## bel.rb + plugins
+  spec.add_runtime_dependency 'bel',               '~> 1.1.0'
+  spec.add_runtime_dependency 'bel-search-sqlite', '~> 1.1.0'
+  spec.add_runtime_dependency 'bel-rdf-jena',      '~> 1.1.0'
 
   ## bel.rb translator dependencies
   spec.add_runtime_dependency 'json-ld',           '2.0.0'
   spec.add_runtime_dependency 'rdf-json',          '2.0.0'
   spec.add_runtime_dependency 'rdf-rdfa',          '2.0.0'
+  spec.add_runtime_dependency 'rdf-xsd',           '2.0.0'
   spec.add_runtime_dependency 'rdf-rdfxml',        '2.0.0'
   spec.add_runtime_dependency 'rdf-trig',          '2.0.0'
   spec.add_runtime_dependency 'rdf-trix',          '2.0.0'
   spec.add_runtime_dependency 'rdf-turtle',        '2.0.0'
 
-  ## bel.rb plugin - annotation/namespace search
-  spec.add_runtime_dependency 'bel-search-sqlite', '~> 1.0.0'
-
-  ## bel.rb plugin - RDF repository using Apache Jena
-  spec.add_runtime_dependency 'bel-rdf-jena',      '~> 1.0.0'
-
   ## Mongo - Faceted search of nanopub.
   spec.add_runtime_dependency 'mongo',             '1.12.5'
   spec.add_runtime_dependency 'bson',              '1.12.5'

data/VERSION

@@ -1 +1 @@
-1.0.4
+1.1.0

data/app/openbel/api/resources/completion.rb

@@ -8,12 +8,12 @@ module OpenBEL
         adapter Oat::Adapters::HAL
         schema do
           type :completion
-          property :type,      item[:type]
-          property :label,     item[:label]
-          property :value,     item[:value]
-          property :highlight, item[:highlight]
-          property :actions,   item[:actions]
-          property :id,        item[:id]
+          property :type,           item[:type]
+          property :id,             item[:id]
+          property :label,          item[:label]
+          property :value,          item[:value]
+          property :caret_position, item[:caret_position]
+          property :validation,     item[:validation]
         end
       end
 
@@ -25,19 +25,11 @@ module OpenBEL
             p.completion item
           end
 
-          link :self,        link_self(item[:id])
           link :describedby, link_described_by(item[:type], item[:id])
         end
 
         private
 
-        def link_self(id)
-          {
-            :type => 'completion',
-            :href => "#{base_url}/api/expressions/#{id}/completions"
-          }
-        end
-
         def link_described_by(type, id)
           case type
           when :function
@@ -55,6 +47,11 @@ module OpenBEL
               :type => 'namespace_value',
               :href => "#{base_url}/api/namespaces/hgnc/#{id}"
             }
+          when :relationship
+            {
+              :type => 'relationship',
+              :href => "#{base_url}/api/relationships/#{id}"
+            }
           else
             raise NotImplementedError.new("Unexpected resource type, #{type}")
           end

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

@@ -71,13 +71,23 @@ module OpenBEL
         end
 
         def base_url
-          env['HTTP_X_REAL_BASE_URL'] ||
-            "#{env['rack.url_scheme']}://#{env['SERVER_NAME']}:#{env['SERVER_PORT']}"
+          if env['SERVER_PORT'] == 443
+            scheme = 'https'
+          else
+            scheme = 'http'
+          end
+
+          "#{scheme}://#{env['HTTP_HOST']}"
         end
 
         def url
-          env['HTTP_X_REAL_URL'] ||
-            "#{env['rack.url_scheme']}://#{env['SERVER_NAME']}:#{env['SERVER_PORT']}/#{env['PATH_INFO']}"
+          if env['SERVER_PORT'] == 443
+            scheme = 'https'
+          else
+            scheme = 'http'
+          end
+
+          "#{scheme}://#{env['HTTP_HOST']}/#{env['PATH_INFO']}"
         end
 
         def schema_url(name)

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

@@ -1,9 +1,15 @@
 require 'cgi'
 require 'bel'
 require 'uri'
+require 'bel_parser/ast_filter'
+require 'bel_parser/ast_generator'
+require 'bel_parser/completion'
 require 'bel_parser/expression/model'
 require 'bel_parser/expression/parser'
 require 'bel_parser/expression/validator'
+require 'bel_parser/language/expression_validator'
+require 'bel_parser/language/semantics'
+require 'bel_parser/parsers/serializer'
 require 'bel_parser/resources'
 require 'bel_parser/resource/jena_tdb_reader'
 
@@ -11,6 +17,7 @@ module OpenBEL
   module Routes
 
     class Expressions < Base
+      include BELParser::Parsers
 
       def initialize(app)
         super
@@ -170,7 +177,7 @@ module OpenBEL
         halt 400 unless bel and caret_position
 
         begin
-          completions = BEL::Completion.complete(bel, @spec, @search, @namespaces, caret_position)
+          completions = BELParser::Completion.complete(bel, @spec, @search, @supported_namespaces, caret_position)
         rescue IndexError => ex
           halt(
             400,
@@ -192,13 +199,22 @@ module OpenBEL
         bel     = params[:splat].first
         flatten = as_bool(params[:flatten])
 
-        statement =
-          BELParser::Expression.parse_statements(
-            bel,
-            @spec,
-            @supported_namespaces
-        )
-        halt 404 unless statement
+        begin
+          statement =
+            BELParser::Expression.parse_statements(
+              bel,
+              @spec,
+              @supported_namespaces
+          )
+          halt 404 unless statement
+        rescue Exception => ex
+          halt(
+              422,
+              {'Content-Type' => 'application/json'},
+              render_json({ :status => 422, :status_name => 'UNPROCESSABLE ENTITY', :msg => ex.to_s })
+          )
+        end
+
 
         response.headers['Content-Type'] = 'application/json'
         MultiJson.dump({
@@ -254,13 +270,105 @@ module OpenBEL
       # Produce validation result for BEL expression using the current language.
       get '/api/expressions/*/validation/?' do
         bel = params[:splat].first
-        response.headers['Content-Type'] = 'text/plain'
 
-        @expression_validator.each(
-          StringIO.new("#{bel}\n")
-        ) do |(num, line, ast, result)|
+        if request.accept.any? { |accept| accept.to_s == 'application/json' }
+          filter =
+            BELParser::ASTFilter.new(
+              BELParser::ASTGenerator.new("#{bel}\n"),
+              :simple_statement,
+              :observed_term,
+              :nested_statement
+            )
+          _, _, ast = filter.each.first
+
+          if ast.nil? || ast.empty?
+            response.headers['Content-Type'] = 'application/json'
+            return render_json(
+              {
+                valid_syntax:    false,
+                valid_semantics: false,
+                message:         'Invalid syntax.',
+                warnings:        [],
+                term_signatures: []
+              }
+            )
+          end
+
+          message             = ''
+          terms               = ast.first.traverse.select { |node| node.type == :term }.to_a
+          semantics_functions =
+            BELParser::Language::Semantics.semantics_functions.reject { |fun|
+              fun == BELParser::Language::Semantics::SignatureMapping
+            }
+
+          semantic_warnings =
+            ast
+              .first
+              .traverse
+              .flat_map { |node|
+                semantics_functions.flat_map { |func|
+                  func.map(node, @spec, @supported_namespaces)
+                }
+              }
+              .compact
+
+          if semantic_warnings.empty?
+            valid = true
+          else
+            valid = false
+            message =
+              semantic_warnings.reduce('') { |msg, warning|
+                msg << "#{warning}\n"
+              }
+            message << "\n"
+          end
+
+          urir      = BELParser::Resource.default_uri_reader
+          urlr      = BELParser::Resource.default_url_reader
+          validator = BELParser::Language::ExpressionValidator.new(@spec, @supported_namespaces, urir, urlr)
+          term_semantics =
+            terms.map { |term|
+              term_result = validator.validate(term)
+              valid      &= term_result.valid_semantics?
+              bel_term    = serialize(term)
+
+              unless valid
+                message << "Term: #{bel_term}\n"
+                term_result.invalid_signature_mappings.map { |m|
+                  message << "  #{m}\n"
+                }
+                message << "\n"
+              end
+
+              {
+                term:               bel_term,
+                valid_signatures:   term_result.valid_signature_mappings.map(&:to_s),
+                invalid_signatures: term_result.invalid_signature_mappings.map(&:to_s)
+              }
+            }
+
+          response.headers['Content-Type'] = 'application/json'
+          render_json(
+            {
+              validation: {
+                expression:      bel,
+                valid_syntax:    true,
+                valid_semantics: valid,
+                message:         valid ? 'Valid semantics' : message,
+                warnings:        semantic_warnings.map(&:to_s),
+                term_signatures: term_semantics
+              }
+            }
+          )
+        else
+          response.headers['Content-Type'] = 'text/plain'
+          @expression_validator.each(
+            StringIO.new("#{bel}\n")
+          ) do |(_, _, _, result)|
+            return result.to_s
+          end
 
-          return result.to_s
+          return "Invalid syntax."
         end
       end
     end

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

@@ -21,14 +21,14 @@ module OpenBEL
         mongo = OpenBEL::Settings[:nanopub_store][:mongo]
         @api  = OpenBEL::Nanopub::Nanopub.new(mongo)
 
-        # RdfRepository using Jena
-        @rr = BEL::RdfRepository.plugins[:jena].create_repository(
-          :tdb_directory => OpenBEL::Settings[:resource_rdf][:jena][:tdb_directory]
-        )
+        # RdfRepository using Jena.
+        tdb = OpenBEL::Settings[:resource_rdf][:jena][:tdb_directory]
+        @rr = BEL::RdfRepository.plugins[:jena].create_repository(:tdb_directory => tdb)
+
 
         # Annotations using RdfRepository
-        annotations                    = BEL::Resource::Annotations.new(@rr)
-        @annotation_transform          = AnnotationTransform.new(annotations)
+        @annotations                    = BEL::Resource::Annotations.new(@rr)
+        @annotation_transform          = AnnotationTransform.new(@annotations)
         @annotation_grouping_transform = AnnotationGroupingTransform.new
       end
 
@@ -116,7 +116,7 @@ module OpenBEL
         # Validate BNJ.
         validate_media_type! "application/json"
         nanopub_obj = read_json
-
+        # STDERR.puts "DBG: nanopub_obj Variable config is #{nanopub_obj.inspect}"
         schema_validation = validate_schema(keys_to_s_deep(nanopub_obj), :nanopub)
         unless schema_validation[0]
           halt(
@@ -127,6 +127,7 @@ module OpenBEL
         end
 
         nanopub = ::BEL::Nanopub::Nanopub.create(nanopub_obj[:nanopub])
+        # STDERR.puts "DBG: nanopub Variable config is #{nanopub.inspect}"
 
         # Standardize annotations.
         @annotation_transform.transform_nanopub!(nanopub, base_url)
@@ -135,12 +136,22 @@ module OpenBEL
         facets = map_nanopub_facets(nanopub)
         hash = nanopub.to_h
         hash[:bel_statement] = hash.fetch(:bel_statement, nil).to_s
+
+        # STDERR.puts "DBG: Variable config is #{hash.inspect}"
+
         hash[:facets]        = facets
         _id                  = @api.create_nanopub(hash)
 
         # Return Location information (201).
         status 201
         headers "Location" => "#{base_url}/api/nanopubs/#{_id}"
+        headers "Content-Type" => 'application/json'
+        render_json(
+            {
+                :status => 201,
+                :location => "#{base_url}/api/nanopubs/#{_id}"
+             }
+        )
       end
 
 			get '/api/nanopubs-stream', provides: 'application/json' do

data/app/openbel/api/schemas/nanopub_resource.schema.json

@@ -3,27 +3,28 @@
   "title": "Nanopub Resource",
   "description": "A single nanopub resource.",
   "type": "object",
-  "additionalProperties": false,
   "required": [
     "nanopub"
   ],
   "properties": {
-    "allOf": [
-      {
-        "$ref":"nanopub.schema.json"
-      },
-      {
-        "type": "object",
-        "additionalProperties": false,
-        "required": [
-          "links"
-        ],
-        "properties": {
-          "links": {
-            "type": "object"
+    "nanopub_resource": {
+      "allOf": [
+        {
+          "$ref": "nanopub.schema.json"
+        },
+        {
+          "type": "object",
+          "additionalProperties": false,
+          "required": [
+            "links"
+          ],
+          "properties": {
+            "links": {
+              "type": "object"
+            }
           }
         }
-      }
-    ]
+      ]
+    }
   }
-}
+}

data/config/config.yml

@@ -8,7 +8,7 @@ bel:
   #     (BEL version 1.0 specification)
   #   2.0
   #     (BEL version 2.0 specification)
-  version: 1.0
+  version: 2.0
 
 # Storage of nanopubs through the Mongo database.
 nanopub_store:
@@ -16,7 +16,7 @@ nanopub_store:
 
     # The MongoDB host to connect to. For example if MongoDB's net.bindIp
     # setting is configured as 127.0.0.1 we should be able to connect using
-    # 'localhost'.  We use 'mongodb' for use in the docker-compose file.
+    # 'localhost'.  We use 'mongodb' for use with docker-compose.
     host:                     'mongodb'
 
     # The default MongoDB port. Configured under MongoDB's `net.port` setting.
@@ -56,7 +56,7 @@ resource_rdf:
 # Full-text search over annotation and namespace values using SQLite.
 resource_search:
   sqlite:
-    database_file: '/data/rdf_resources/biological-concepts-rdf.db'
+    database_file: '/data/rdf_resources.db'
 
 # Set a secret used during session creation....
 session_secret: 'changeme'
@@ -66,8 +66,5 @@ auth:
   # Controls whether the API requires authentication
   enabled: false
   # Used by the auth middleware to decode and verify the JWT
-  secret: |
-    -----BEGIN PUBLIC KEY-----
-    MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAu77nUtVw7SIIcUTSiStzMPB7BGB/9eS+CpppsUaiyZyWCXlrALT3YdqneSlpX4Ta+0wvhOkKQtoSS8dCH8GIi7esAmfdHetHfRgeDXHAlXo8HIzshUzODg3ysT7j+Ha3eJsO+LNS/omHDhsarP8Z2eThW876iKJCCc/mB76a6u1e4Id+52K5lG++m8Pn4Gs+cqd2sKUKcMJ9CkJ6dBIdGlXHMoOHj4C33SPrEG/vEBv5cu0l5PP3RiBAuaZHpLKzfIiaLOpj/k4dD/weVt5gwTIJn16AEgPD7173Xef0HgoPlQInDFrJwsGpYCnIPZWSxRbvjKkya2Auj0QZyMCrXwIDAQAB
-    -----END PUBLIC KEY-----
+  #secret:   'JWT secret here'
 

metadata

@@ -1,348 +1,362 @@
 --- !ruby/object:Gem::Specification
 name: openbel-api
 version: !ruby/object:Gem::Version
-  version: 1.0.4
+  version: 1.1.0
 platform: java
 authors:
 - Anthony Bargnesi
 - Nick Bargnesi
 - William Hayes
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2016-03-23 00:00:00.000000000 Z
+date: 2017-01-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: bel
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.0.0
-  type: :runtime
+        version: 1.1.0
+  name: bel
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: 1.1.0
 - !ruby/object:Gem::Dependency
-  name: json-ld
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.0.0
+        version: 1.1.0
+  name: bel-search-sqlite
+  prerelease: false
   type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.1.0
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.1.0
+  name: bel-rdf-jena
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.0.0
+        version: 1.1.0
 - !ruby/object:Gem::Dependency
-  name: rdf-json
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
-  type: :runtime
+  name: json-ld
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
-  name: rdf-rdfa
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
-  type: :runtime
+  name: rdf-json
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
-  name: rdf-rdfxml
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
-  type: :runtime
+  name: rdf-rdfa
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
-  name: rdf-trig
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
-  type: :runtime
+  name: rdf-xsd
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
-  name: rdf-trix
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
-  type: :runtime
+  name: rdf-rdfxml
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
-  name: rdf-turtle
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
-  type: :runtime
+  name: rdf-trig
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 2.0.0
 - !ruby/object:Gem::Dependency
-  name: bel-search-sqlite
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
-        version: 1.0.0
-  type: :runtime
+        version: 2.0.0
+  name: rdf-trix
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
-  name: bel-rdf-jena
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
-        version: 1.0.0
-  type: :runtime
+        version: 2.0.0
+  name: rdf-turtle
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
-  name: mongo
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.12.5
-  type: :runtime
+  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
-  name: bson
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.12.5
-  type: :runtime
+  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
-  name: dot_hash
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.5.9
-  type: :runtime
+  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
-  name: jrjackson
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.3.7
-  type: :runtime
+  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
-  name: json_schema
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.10.0
-  type: :runtime
+  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
-  name: multi_json
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.11.2
-  type: :runtime
+  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
-  name: oat
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.4.6
-  type: :runtime
+  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
-  name: puma
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 3.1.0
-  type: :runtime
+  name: puma
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 3.1.0
 - !ruby/object:Gem::Dependency
-  name: rack
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.6.4
-  type: :runtime
+  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
-  name: rack-cors
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.4.0
-  type: :runtime
+  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
-  name: rack-handlers
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 0.7.0
-  type: :runtime
+  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
-  name: sinatra
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.4.6
-  type: :runtime
+  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
-  name: sinatra-contrib
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.4.6
-  type: :runtime
+  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
-  name: jwt
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
         version: 1.5.2
-  type: :runtime
+  name: jwt
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
@@ -351,9 +365,9 @@ dependencies:
 description: The OpenBEL API provides a RESTful API over HTTP to manage BEL knowledge.
 email: abargnesi@selventa.com
 executables:
+- setup-docker.sh
 - openbel-api
 - openbel-config
-- setup-docker.sh
 extensions: []
 extra_rdoc_files: []
 files:
@@ -434,7 +448,7 @@ homepage: https://github.com/OpenBEL/openbel-api
 licenses:
 - Apache-2.0
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - app
@@ -450,9 +464,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.4.6
-signing_key: 
+rubyforge_project:
+rubygems_version: 2.6.8
+signing_key:
 specification_version: 4
 summary: The OpenBEL API provided over RESTful HTTP endpoints.
 test_files: []