openbel-api 0.4.0-java → 0.5.0-java

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 84860112a47f326439806c8f6f81987e31a47121
-  data.tar.gz: 55a1281b0db90eae0ba49b6314d3727c29225268
+  metadata.gz: 51e6f9a762021d8b56fd1bf8a2dfe97a42c97b98
+  data.tar.gz: 3f83ea9644a89fc9c019858594ebe6e31507a4b2
 SHA512:
-  metadata.gz: 1a3d631752e68f0be2686c1bf8eb4efa13b19f803fe9dc9a1572a3171f36f881904e5c5279e537587ee9005c49fa12c5ff61cff096ac142f42d870eb5e653562
-  data.tar.gz: 094034e7a35004b6e05da1174cad42e1b372a77e526159a939891824e2c20e309a658a15084a001551b9caafd1fc6c68ec6d06cd485dbe0f67c0a1c81762be41
+  metadata.gz: ada40940474506e44d79afb3300733149a363716b7d2bc8bf8232a3264079fd91f85b58ab8363554ff0f3a96c686e270f93f4eb907cbb789b9fa8bf9fce35d8a
+  data.tar.gz: 0166d8e47e7db5f1354df5cd7c8e6740f2da365d4f34747e4aabc6f7431eb9cfa21c83aed9e333ee11576c87529ccca5635fef8c04bf62e1a60ee75123bd2848

data/.gemspec

@@ -1,6 +1,8 @@
 Gem::Specification.new do |spec|
   spec.name                  = 'openbel-api'
-  spec.version               = '0.4.0'
+  spec.version               = File.read(
+                                 File.join(File.expand_path(File.dirname(__FILE__)), 'VERSION')
+                               )
   spec.summary               = %q{The OpenBEL API provided over RESTful HTTP endpoints.}
   spec.description           = %q{The OpenBEL API provides a RESTful API over HTTP to manage BEL knowledge.}
   spec.license               = 'Apache-2.0'
@@ -9,13 +11,14 @@ Gem::Specification.new do |spec|
                                  'Nick Bargnesi',
                                  'William Hayes'
                                ]
-  spec.date                  = %q{2015-12-02}
+  spec.date                  = %q{2015-12-17}
   spec.email                 = %q{abargnesi@selventa.com}
   spec.files                 = [
                                  Dir.glob('app/**/*.{json,rb,ru}'),
                                  Dir.glob('config/**/*.{rb,yml}'),
                                  Dir.glob('lib/**/*.rb'),
                                  __FILE__,
+                                 'VERSION',
                                  'CHANGELOG.md',
                                  'LICENSE',
                                  'INSTALL.md',
@@ -31,13 +34,13 @@ Gem::Specification.new do |spec|
   # Dependencies
 
   ## bel.rb
-  spec.add_runtime_dependency 'bel',               '0.4.0'
+  spec.add_runtime_dependency 'bel',               '0.4.1'
 
   ## bel.rb plugin - annotation/namespace search
-  spec.add_runtime_dependency 'bel-search-sqlite', '0.4.0'
+  spec.add_runtime_dependency 'bel-search-sqlite', '0.4.2'
 
   ## bel.rb plugin - RDF repository using Apache Jena
-  spec.add_runtime_dependency 'bel-rdf-jena',      '0.4.0'
+  spec.add_runtime_dependency 'bel-rdf-jena',      '0.4.1'
 
   ## RDF - RDF abstraction
   spec.add_runtime_dependency 'rdf',               '1.99.0'

data/CHANGELOG.md

@@ -3,7 +3,22 @@ All notable changes to openbel-api will be documented in this file. The curated
 
 This project adheres to [Semantic Versioning][Semantic Versioning].
 
-## [0.4.0][0.4.0] - 2015-12-14
+## [0.5.0][0.5.0] - 2015-12-17
+### Added
+- Report API version from executables (`openbel-api`, `openbel-config`) and REST API (`GET /api/version`) ([Issue #91][91]).
+- Support for MongoDB user authentication ([Issue #92][92]).
+  - See [MongoDB User Authentication][MongoDB User Authentication].
+
+### Changed
+- Namespace value autocompletion will not return identifier-based namespace (e.g. Entrez Gene) suggestions unless the namespace prefix is used. For example "p(AKT" will not suggest "EGID:207" although "p(EG:AKT" will.
+
+### Fixed
+- Namespace value autocompletion will return the namespace prefix if the BEL term requires it. For example "p(AKT" will now suggest "HGNC:AKT1".
+- Namespace value autocompletion now queries against the Resource RDF to lookup namespaces by prefix. Previously this resolves namespaces from hardcoded values in bel.rb.
+
+-----
+
+## 0.4.0 - 2015-12-14
 ### Added
 - Evidence Store
   - Storage of evidence including creation, retrieval, modification, and deletion actions.
@@ -19,4 +34,8 @@ This project adheres to [Semantic Versioning][Semantic Versioning].
   - Retrieve equivalent namespace values from the individual.
   - Retrieve orthologous namespace values from the individual.
 
-[Semantic Versioning]: http://semver.org
+[0.5.0]:                       https://github.com/OpenBEL/openbel-api/compare/0.4.0...0.5.0
+[Semantic Versioning]:         http://semver.org
+[MongoDB User Authentication]: https://github.com/OpenBEL/openbel-api/wiki/Configuring-the-Evidence-Store#mongodb-user-authentication
+[91]:                          https://github.com/OpenBEL/openbel-api/issues/91
+[92]:                          https://github.com/OpenBEL/openbel-api/issues/92

data/README.md

@@ -51,8 +51,9 @@ The OpenBEL API is built to run with [JRuby][JRuby] and [Java 8][Java 8].
 *System Requirements*
 
 - [Java 8][Java 8]
-- [JRuby][JRuby], 1.7.x or 9.x series (9.0.x.0 is recommended)
-  - Follow [JRuby Getting Started][JRuby Getting Started] for installation instructions.
+- [JRuby][JRuby], 9.x series (9.0.x.0 is recommended)
+  - The 9.x series is required due to a Ruby language 2.0 requirement.
+  - See "Installation" below for configuring JRuby and isolating the openbel-api application.
 - [MongoDB][MongoDB], version 3.0 or greater
   - Follow [MongoDB download][MongoDB download] page for download and installation instructions.
 - [SQLite][SQLite], version 3.8.0 or greater
@@ -64,6 +65,25 @@ The OpenBEL API is built to run with [JRuby][JRuby] and [Java 8][Java 8].
 
 The OpenBEL API is packaged and installed as a Ruby gem. A Ruby gem is packed library or application that runs on the Ruby virtual machine. In this case OpenBEL API runs only on [JRuby][JRuby].
 
+#### JRuby Configuration
+
+- Unpack JRuby archive.
+- Export the JRUBY_HOME environment variable to the unpacked JRuby archive directory.
+- Add "$JRUBY_HOME/bin" to your PATH environment variable.
+- Export the GEM_HOME and GEM_PATH environment variable to any directory accessible to the current user. This is where JRuby gems will be installed. The OpenBEL API and dependencies will be installed into this directory for isolation from other Ruby applications running on the system.
+
+*Example JRuby Configuration*
+
+Assume that we have unpacked JRuby to `/opt/jruby`. We should then:
+
+- Export `JRUBY_HOME` to `/opt/jruby`.
+- Add `$JRUBY_HOME/bin` to our `PATH` environment variable.
+- Export both `GEM_HOME` and `GEM_PATH` to `/opt/jruby/gems`.
+- Add `$GEM_HOME/bin` to our `PATH` environment variable.
+- Proceed with *Installation of OpenBEL API*.
+
+#### Installation of OpenBEL API
+
 Installation uses the [RubyGems][RubyGems] site to download and install the gem from. To install the OpenBEL API gem run the `gem install` command available within your [JRuby][JRuby] installation.
 
 ```bash
@@ -72,6 +92,9 @@ gem install openbel-api
 
 All of the application dependencies needed by `openbel-api` will be installed during this process.
 
+**Tip**
+If the `openbel-api` executable is not available make sure `$GEM_HOME/bin` is included on your `PATH`. See *JRuby Configuration* above.
+
 ### Configuration
 
 The OpenBEL API requires a configuration file to set up a few things. You can create an initial configuration file using the `openbel-config` command.
@@ -93,6 +116,8 @@ evidence_store:
     database: 'openbel'
 ```
 
+There are also settings for user authentication. See [MongoDB User Authentication][MongoDB User Authentication] on the wiki.
+
 *Resource RDF data*
 Annotations, namespaces, and dataset storage are represented as [RDF][RDF] data. The data is stored in an on-disk database using Apache Jena (Java library included with `openbel-api`).
 
@@ -176,9 +201,36 @@ openbel-api --file openbel-api-config.yml -- --port 9000 --threads 1:16
 **Note**
 Run `openbel-api --help` for more information and options.
 
+### Running behind Nginx (or another reverse proxy)
+
+The OpenBEL API beings at the `/api` path. If you plan OpenBEL API behing a reverse proxy then you will want to setup a route to `/api`.
+
+For example the following [Nginx][Nginx] configuration will proxy from `http://$hostname/api` to `http://localhost:9000/api`.
+
+```
+server {
+    listen        0.0.0.0:80;
+    server_name   $hostname;
+    access_log    /var/log/nginx/access.log main;
+    error_log     /var/log/nginx/error.log info;
+
+    location /api {
+        proxy_pass               http://localhost:9000;
+        proxy_set_header         Host $host;
+        proxy_set_header         X-Real-IP $remote_addr;
+        proxy_set_header         X-Real-Base-URL $scheme://$host;
+        proxy_set_header         X-Real-URL $scheme://$host$request_uri;
+        proxy_buffer_size        128k;
+        proxy_buffers            4 256k;
+        proxy_busy_buffers_size  256k;
+        client_max_body_size     50M;
+    }
+}
+```
+
 ## API Documentation
 
-The REST API is defined by a [RAML][RAML] specification. The specification is published [here][OpenBEL API RAML specification].
+The REST API is defined by a [RAML][RAML] specification. Th                is published [here][OpenBEL API RAML specification].
 
 API documentation with *Try it* functionality is available [here][OpenBEL API documentation].
 
@@ -205,4 +257,5 @@ Built with collaboration and :heart: by the [OpenBEL][OpenBEL] community.
 [Puma HTTP server]: http://puma.io/
 [Resource RDF 20150611]: http://build.openbel.org/browse/OR-RRD2/latestSuccessful/artifact
 [Resource Search 20150611]: http://build.openbel.org/browse/OR-RSD2/latestSuccessful/artifact
-
+[Nginx]: http://nginx.org/
+[MongoDB User Authentication]: https://github.com/OpenBEL/openbel-api/wiki/Configuring-the-Evidence-Store#mongodb-user-authentication

data/VERSION

@@ -0,0 +1 @@
+0.5.0

data/app/openbel/api/app.rb

@@ -10,6 +10,7 @@ require 'sinatra/base'
 require "sinatra/reloader"
 require "sinatra/cookies"
 
+require_relative 'version'
 require_relative 'config'
 require_relative 'routes/base'
 require_relative 'routes/root'
@@ -20,6 +21,7 @@ require_relative 'routes/expressions'
 require_relative 'routes/functions'
 require_relative 'routes/namespaces'
 require_relative 'routes/authenticate'
+require_relative 'routes/version'
 require_relative 'middleware/auth'
 
 module OpenBEL
@@ -65,6 +67,7 @@ module OpenBEL
 
     # routes not requiring authentication
     use OpenBEL::Routes::Root
+    use OpenBEL::Routes::Version
     use OpenBEL::Routes::Annotations
     use OpenBEL::Routes::Expressions
     use OpenBEL::Routes::Functions

data/app/openbel/api/config.rb

@@ -22,7 +22,10 @@ module OpenBEL
         if block_given?
           yield failure[1]
         else
-          fail "Configuration error: #{failure[1]}"
+          fail(<<-ERR.gsub(/^\s+/, ''))
+            Configuration error within #{File.expand_path(config_file)}:
+            #{failure[1]}
+          ERR
         end
       end
 
@@ -32,9 +35,94 @@ module OpenBEL
     private
 
     def self.validate(cfg)
+      # validate evidence_store block
+      evidence_store = cfg[:evidence_store]
+      unless evidence_store
+        return [
+          true, <<-ERR
+            An "evidence_store" is not configured.
+            #{boilerplate_help}
+          ERR
+        ]
+      end
+      evidence_failure = self.validate_evidence_store(cfg[:evidence_store])
+      return evidence_failure if evidence_failure
+
       nil
     end
 
+    def self.validate_evidence_store(evidence_store)
+      mongo = evidence_store[:mongo]
+      unless mongo
+        return [
+          true, <<-ERR
+            The "evidence_store.mongo" configuration block is not configured.
+            #{boilerplate_help}
+          ERR
+        ]
+      end
+
+      required = [:host, :port, :database]
+
+      required.each do |setting|
+        unless mongo[setting]
+          return [
+            true, <<-ERR
+              The "evidence_store.mongo.#{setting}" setting is not configured.
+              #{boilerplate_help}
+            ERR
+          ]
+        end
+      end
+
+      # Test connection to the MongoDB instance.
+      require 'mongo'
+      begin
+        mongo_client = Mongo::MongoClient.new(mongo[:host], mongo[:port])
+        mongo_client.connect
+      rescue Mongo::ConnectionFailure => e
+        return [
+          true, <<-ERR
+            Unable to connect to MongoDB at host "#{mongo[:host]}" and port "#{mongo[:port]}".
+            #{boilerplate_help}
+
+            MongoDB error:
+            #{e}
+          ERR
+        ]
+      end
+
+      # Attempt access of database.
+      db = mongo_client.db(mongo[:database])
+
+      # Authenticate user if provided.
+      if mongo[:username] && mongo[:password]
+        auth_db = mongo[:authentication_database] || mongo[:database]
+        begin
+          db.authenticate(mongo[:username], mongo[:password], nil, auth_db)
+        rescue Mongo::AuthenticationError => e
+          return [
+            true, <<-ERR
+              Unable to authenticate "#{mongo[:username]}" against the "#{auth_db}" authentication database.
+              #{boilerplate_help}
+
+              MongoDB error:
+              #{e}
+            ERR
+          ]
+        end
+      end
+
+      nil
+    end
+
+    def self.boilerplate_help
+      <<-ERR.gsub(/^\s+/, '')
+        Run the "openbel-config" command to see an example configuration.
+        See https://github.com/OpenBEL/openbel-api/wiki/Configuring-the-Evidence-Store for details on how to configure an Evidence Store.
+      ERR
+    end
+
     class SilentProperties < Properties
       def method_missing(key, *args, &block)
         return nil unless has_key?(key)

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

@@ -84,8 +84,9 @@ module OpenBEL
         halt 404 unless match.length > 1
 
         match_results  = @search.search(wildcard_match(match), :annotation_concept, nil, nil,
-          :start => start,
-          :size => size
+          :start                      => start,
+          :size                       => size,
+          :exclude_identifier_schemes => false
         ).map { |result|
           value = OpenBEL::Resource::Annotations::AnnotationValueSearchResult.new(@rr, result.uri)
           value.match_text = result.snippet
@@ -131,8 +132,9 @@ module OpenBEL
         halt 404 unless match.length > 1
 
         match_results = @search.search(wildcard_match(match), :annotation_concept, annotation.uri.to_s, nil,
-          :start => start,
-          :size => size
+          :start                      => start,
+          :size                       => size,
+          :exclude_identifier_schemes => false
         ).map { |result|
           value = OpenBEL::Resource::Annotations::AnnotationValueSearchResult.new(@rr, result.uri)
           value.match_text = result.snippet

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

@@ -49,12 +49,6 @@ module OpenBEL
 
       disable :protection
 
-      before do
-        unless request.preferred_type(SPOKEN_CONTENT_TYPES)
-          halt 406
-        end
-      end
-
       helpers do
 
         def as_bool(value)

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

@@ -28,11 +28,8 @@ module OpenBEL
         super
 
         # Evidence API using Mongo.
-        @api = OpenBEL::Evidence::Evidence.new(
-          :host     => OpenBEL::Settings[:evidence_store][:mongo][:host],
-          :port     => OpenBEL::Settings[:evidence_store][:mongo][:port],
-          :database => OpenBEL::Settings[:evidence_store][:mongo][:database]
-        )
+        mongo = OpenBEL::Settings[:evidence_store][:mongo]
+        @api  = OpenBEL::Evidence::Evidence.new(mongo)
 
         # RdfRepository using Jena.
         @rr = BEL::RdfRepository.plugins[:jena].create_repository(

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

@@ -16,11 +16,8 @@ module OpenBEL
       def initialize(app)
         super
 
-        @api = OpenBEL::Evidence::Evidence.new(
-          :host     => OpenBEL::Settings[:evidence_store][:mongo][:host],
-          :port     => OpenBEL::Settings[:evidence_store][:mongo][:port],
-          :database => OpenBEL::Settings[:evidence_store][:mongo][:database]
-        )
+        mongo = OpenBEL::Settings[:evidence_store][:mongo]
+        @api  = OpenBEL::Evidence::Evidence.new(mongo)
 
         # RdfRepository using Jena
         @rr = BEL::RdfRepository.plugins[:jena].create_repository(

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

@@ -123,7 +123,7 @@ module OpenBEL
         halt 400 unless bel and caret_position
 
         begin
-          completions = BEL::Completion.complete(bel, @search, caret_position)
+          completions = BEL::Completion.complete(bel, @search, @namespaces, caret_position)
         rescue IndexError => ex
           halt(
             400,

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

@@ -118,8 +118,9 @@ module OpenBEL
         halt 404 unless match.length > 1
 
         match_results = @search.search(wildcard_match(match), :namespace_concept, nil, nil,
-          :start => start,
-          :size => size
+          :start                      => start,
+          :size                       => size,
+          :exclude_identifier_schemes => false
         ).map { |result|
           value = OpenBEL::Resource::Namespaces::NamespaceValueSearchResult.new(@rr, result.uri)
           value.match_text = result.snippet
@@ -169,8 +170,9 @@ module OpenBEL
         halt 404 unless match.length > 1
 
         match_results = @search.search(wildcard_match(match), :namespace_concept, namespace.uri.to_s, nil,
-          :start => start,
-          :size => size
+          :start                      => start,
+          :size                       => size,
+          :exclude_identifier_schemes => false
         ).map { |result|
           value = OpenBEL::Resource::Namespaces::NamespaceValueSearchResult.new(@rr, result.uri)
           value.match_text = result.snippet

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

@@ -0,0 +1,49 @@
+require_relative '../version'
+require 'rack/mime'
+
+module OpenBEL
+  module Routes
+
+    class Version < Base
+
+      JSON             = Rack::Mime.mime_type('.json')
+      TEXT             = Rack::Mime.mime_type('.txt')
+      ACCEPTED_TYPES   = {'json' => JSON, 'text' => TEXT}
+      DEFAULT_TYPE     = TEXT
+
+      options '/api/version' do
+        response.headers['Allow'] = 'OPTIONS,GET'
+        status 200
+      end
+
+      get '/api/version' do
+        accept_type = request.accept.find { |accept_entry|
+          ACCEPTED_TYPES.values.include?(accept_entry.to_s)
+        }
+        accept_type ||= DEFAULT_TYPE
+
+        format = params[:format]
+        if format
+          accept_type = ACCEPTED_TYPES[format]
+          halt 406 unless accept_type
+        end
+
+        if accept_type == JSON
+          render_json(
+            {
+              :version => {
+                :string                    => OpenBEL::Version.to_s,
+                :semantic_version_numbers  => OpenBEL::Version.to_a
+              }
+            }
+          )
+        else
+          response.headers['Content-Type'] = 'text/plain'
+          OpenBEL::Version.to_s
+        end
+      end
+    end
+  end
+end
+# vim: ts=2 sw=2:
+# encoding: utf-8

data/app/openbel/api/version.rb

@@ -0,0 +1,38 @@
+module OpenBEL
+
+  # Captures the version of the OpenBEL API.
+  module Version
+
+    # The frozen version {String}. See {Object#freeze}.
+    STRING              = File.read(
+                            File.join(
+                              File.expand_path(File.dirname(__FILE__)),
+                              '..', '..','..',
+                              'VERSION'
+                            )
+                          ).chomp.freeze
+
+    # The frozen {Fixnum version numbers}. See {Object#freeze}.
+    MAJOR, MINOR, PATCH = STRING.split('.').map(&:freeze)
+
+    # The frozen {Array} of {Fixnum version numbers}. See {Object#freeze}.
+    VERSION_NUMBERS     = [MAJOR, MINOR, PATCH].freeze
+
+    # Add singleton methods to the metaclass of {OpenBEL::Version}.
+    class << self
+
+      # Return the frozen, semantic version {String} for the OpenBEL API.
+      # @return [frozen String] the semantic version of the OpenBEL API
+      def to_s
+        STRING
+      end
+      alias :to_str :to_s
+
+      # Return the frozen, semantic version number {Array} for the OpenBEL API.
+      # @return [frozen Array] the semantic version numbers of the OpenBEL API
+      def to_a
+        VERSION_NUMBERS
+      end
+    end
+  end
+end

data/bin/openbel-api

@@ -52,6 +52,13 @@ OpenBEL API Options
 	opts.on('-f', '--file FILE', 'The file where the configuration will be written.') do |file|
 		options[:file] = file
 	end
+
+  opts.on('-v', '--version', 'The version of the OpenBEL API.') do
+    require 'openbel/api/version'
+
+    $stdout.puts OpenBEL::Version
+    exit
+  end
 end
 
 parser.default_argv = OPENBEL_ARGV
@@ -61,6 +68,15 @@ if options[:file]
 	config_file = options[:file]
 end
 
+unless config_file
+  $stderr.puts <<-ERR.gsub(/^\s+/, '')
+    The OpenBEL API configuration file was not set.
+    Run the "openbel-api --help" command to review the options for setting the configuration file.
+    See https://github.com/OpenBEL/openbel-api/wiki/OpenBEL-API-Config for further details on the OpenBEL API configuration file.
+  ERR
+  exit 1
+end
+
 begin
 	File.open(config_file, 'r')
 rescue SystemCallError => err

data/bin/openbel-config

@@ -15,6 +15,13 @@ OptionParser.new do |opts|
   opts.on('-f', '--file FILE', 'The file where the configuration will be written.') do |file|
     options[:file] = file
   end
+
+  opts.on('-v', '--version', 'The version of the OpenBEL API.') do
+    require 'openbel/api/version'
+
+    $stdout.puts OpenBEL::Version
+    exit
+  end
 end.parse!
 
 # resolve path for config.yml template

data/config/config.yml

@@ -3,9 +3,40 @@
 # Storage of evidence through the Mongo database.
 evidence_store:
   mongo:
-    host:     'localhost'
-    port:     27017
-    database: 'openbel'
+
+    # 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.
+    host:                     'localhost'
+
+    # The default MongoDB port. Configured under MongoDB's `net.port` setting.
+    port:                     27017
+
+    # The name of your database. We think "openbel-evidence" should be fine,
+    # but it's up to you.
+    database:                 'openbel-evidence'
+
+    # MongoDB authentication and role assignment. These settings are necessary
+    # if you would like to have a MongoDB user authenticated and authorized to
+    # use the configure database.
+
+    #First, you will need to create a MongoDB user with the "readWrite" and
+    #"dbAdmin" roles for the "database" value set above. This is to allow read,
+    #write, and index creation in the OpenBEL API application.
+    #See https://github.com/OpenBEL/openbel-api/wiki/Configuring-the-Evidence-Store#adding-the-openbel-user
+    #username:                'openbel-user'
+
+    #Second, you will need to set a password for the MongoDB user set above.
+    #MongoDB passwords are hashed using SCRAM-SHA-1 on the client and server.
+    #This is the default hashing strategy on MongoDB 3.0 and after.
+    #See https://docs.mongodb.org/v3.0/core/security-scram-sha-1/
+    #password:                'changeme'
+
+    # If your MongoDB users are managed in a separate Mongo database then you
+    # will need to set it here. This can be useful if you are managing users in
+    # a separate Mongo database from the application's database.
+    # Optional; defaults to the "database" set above.
+    #authentication_database: 'openbel'
 
 # RDF dataset for BEL datasets, annotations, and namespaces using Apache Jena.
 resource_rdf:

data/lib/openbel/api/evidence/mongo.rb

@@ -11,10 +11,19 @@ module OpenBEL
       include Mongo
 
       def initialize(options = {})
-        host             = options.delete(:host)
-        port             = options.delete(:port)
-        db               = options.delete(:database)
+        host             = options[:host]
+        port             = options[:port]
+        db               = options[:database]
         @db              = MongoClient.new(host, port).db(db)
+
+        # Authenticate user if provided.
+        username = options[:username]
+        password = options[:password]
+        if username && password
+          auth_db = options[:authentication_database] || db
+          @db.authenticate(username, password, nil, auth_db)
+        end
+
         @collection      = @db[:evidence]
         @collection.ensure_index(
           {:"bel_statement" => Mongo::ASCENDING },

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: openbel-api
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.5.0
 platform: java
 authors:
 - Anthony Bargnesi
@@ -10,14 +10,14 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2015-12-02 00:00:00.000000000 Z
+date: 2015-12-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 0.4.0
+        version: 0.4.1
   name: bel
   prerelease: false
   type: :runtime
@@ -25,13 +25,13 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 0.4.0
+        version: 0.4.1
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 0.4.0
+        version: 0.4.2
   name: bel-search-sqlite
   prerelease: false
   type: :runtime
@@ -39,13 +39,13 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 0.4.0
+        version: 0.4.2
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 0.4.0
+        version: 0.4.1
   name: bel-rdf-jena
   prerelease: false
   type: :runtime
@@ -53,7 +53,7 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: 0.4.0
+        version: 0.4.1
 - !ruby/object:Gem::Dependency
   requirement: !ruby/object:Gem::Requirement
     requirements:
@@ -292,6 +292,7 @@ files:
 - INSTALL_RUBY.md
 - LICENSE
 - README.md
+- VERSION
 - app/openbel/api/app.rb
 - app/openbel/api/config.rb
 - app/openbel/api/config.ru
@@ -315,6 +316,7 @@ files:
 - app/openbel/api/routes/functions.rb
 - app/openbel/api/routes/namespaces.rb
 - app/openbel/api/routes/root.rb
+- app/openbel/api/routes/version.rb
 - app/openbel/api/schemas.rb
 - app/openbel/api/schemas/annotation_collection.schema.json
 - app/openbel/api/schemas/annotation_resource.schema.json
@@ -328,6 +330,7 @@ files:
 - app/openbel/api/schemas/namespace_value_collection.schema.json
 - app/openbel/api/schemas/namespace_value_resource.schema.json
 - app/openbel/api/util.rb
+- app/openbel/api/version.rb
 - bin/openbel-api
 - bin/openbel-config
 - config/async_evidence.rb