openbel-api 0.5.1-java → 0.6.1-java

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 1e92506a6a1b43f887a0b8a0b90a89e79784aa1c
-  data.tar.gz: a460b94a82a4430ffcd3a24c627fae818ca30c81
+  metadata.gz: 1fa47f8991f91aad490818b0c6e6a5fc8f822ecc
+  data.tar.gz: bbd5f02dfa6c64f060181b029d138960a9ef691f
 SHA512:
-  metadata.gz: a2c221355ede69af12b3cce38a99d70126cfa763aed4dfdc6674783724220066711ad5c4a903e6b15320d46f950b6c091406dad8f031f3c09a4fb2d1b44b90e0
-  data.tar.gz: edad2faa9587a091ba86baca74c6446dbb489430efdb3f485153b5eaf5dce142dc4b0a4b8bd4b8dbae7eff822a969c0117b5f711e99fb60663bc60913212d0cf
+  metadata.gz: d2fe0173aad3c83200e69361bcd632ee38d19d6b52465f63678fd3385f792cfc491841bee631f4229289e43e843ac3e8e05dddec99d8a64f35508775574a390d
+  data.tar.gz: 28c72b97ae6f3eb3381f51a4194a16b84760549a07c3bcfb31ca7c9a05bfb824f55418d5d3f9fd4017e0d63df2d119a05a27856b6cd4b192909bdfe1a5a9bf21

data/.gemspec

@@ -11,7 +11,7 @@ Gem::Specification.new do |spec|
                                  'Nick Bargnesi',
                                  'William Hayes'
                                ]
-  spec.date                  = %q{2015-12-18}
+  spec.date                  = %q{2016-03-16}
   spec.email                 = %q{abargnesi@selventa.com}
   spec.files                 = [
                                  Dir.glob('app/**/*.{json,rb,ru}'),
@@ -34,16 +34,25 @@ Gem::Specification.new do |spec|
   # Dependencies
 
   ## bel.rb
-  spec.add_runtime_dependency 'bel',               '0.4.1'
+  spec.add_runtime_dependency 'bel',               '0.6.0'
+
+  ## bel.rb translator dependencies
+  spec.add_runtime_dependency 'json-ld',           '1.99.0'
+  spec.add_runtime_dependency 'rdf-json',          '1.99.0'
+  spec.add_runtime_dependency 'rdf-rdfa',          '1.99.0'
+  spec.add_runtime_dependency 'rdf-rdfxml',        '1.99.0'
+  spec.add_runtime_dependency 'rdf-trig',          '1.99.0.1'
+  spec.add_runtime_dependency 'rdf-trix',          '1.99.0'
+  spec.add_runtime_dependency 'rdf-turtle',        '1.99.0'
 
   ## bel.rb plugin - annotation/namespace search
   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',      '0.4.1'
+  spec.add_runtime_dependency 'bel-rdf-jena',      '0.4.2'
 
   ## RDF - RDF abstraction
-  spec.add_runtime_dependency 'rdf',               '1.99.0'
+  spec.add_runtime_dependency 'rdf',               '1.99.1'
 
   ## Mongo - Faceted search of evidence.
   spec.add_runtime_dependency 'mongo',             '1.12.5'
@@ -55,14 +64,13 @@ Gem::Specification.new do |spec|
   spec.add_runtime_dependency 'json_schema',       '0.10.0'
   spec.add_runtime_dependency 'multi_json',        '1.11.2'
   spec.add_runtime_dependency 'oat',               '0.4.6'
-  spec.add_runtime_dependency 'puma',              '2.15.3'
+  spec.add_runtime_dependency 'puma',              '3.1.0'
   spec.add_runtime_dependency 'rack',              '1.6.4'
   spec.add_runtime_dependency 'rack-cors',         '0.4.0'
   spec.add_runtime_dependency 'rack-handlers',     '0.7.0'
   spec.add_runtime_dependency 'sinatra',           '1.4.6'
   spec.add_runtime_dependency 'sinatra-contrib',   '1.4.6'
   spec.add_runtime_dependency 'jwt',               '1.5.2'
-  spec.add_runtime_dependency 'rest-client',       '1.8.0'
 end
 # vim: ts=2 sw=2:
 # encoding: utf-8

data/CHANGELOG.md

@@ -3,10 +3,36 @@ All notable changes to openbel-api will be documented in this file. The curated
 
 This project adheres to [Semantic Versioning][Semantic Versioning].
 
+## [0.6.1][0.6.1] - 2016-03-16
+### Changed
+- Bumped gems specification date. Requires new version because 0.6.0 was yanked from RubyGems.
+
+## [0.6.0][0.6.0] - 2016-03-16
+### Added
+- Retrieve evidence in a format supported by BEL translator plugins ([Issue 44][44]).
+- Retrieve dataset evidence in a format supported by BEL translator plugins ([Issue 99][99]).
+
+### Fixed
+- Dataset evidence collection is missing annotation/namespace URIs ([Issue 95][95]).
+- Facets are not created for evidence uploaded through a dataset.
+
+### Changed
+- MongoDB version 3.2.0 is now required due to use of `$slice` operator in Aggregation queries.
+
+### Known Issue
+Datasets are stored with a URI computed from the scheme and host that is serving the OpenBEL API. For example if OpenBEL API is served from `http://web.site.com` then dataset URIs will be of the form `http://web.site.com/api/datasets/{UUID}`. If you change the scheme and host these URIs will be inconsistent and you will not be able to retrieve your datasets. You will have to re-import your documents.
+
+  - See [Issue #102][102].
+
+-----
+
 ## [0.5.1][0.5.1] - 2015-12-18
 ### Fixed
 - Authentication error for MongoDB user when faceting on `GET /api/evidence` ([Issue #93][93]).
 
+### Changed
+- MongoDB version 3.2.0 is now required due to use of `$slice` operator in Aggregation queries ([Issue ?][]).
+
 -----
 
 ## [0.5.0][0.5.0] - 2015-12-17
@@ -40,10 +66,16 @@ This project adheres to [Semantic Versioning][Semantic Versioning].
   - Retrieve equivalent namespace values from the individual.
   - Retrieve orthologous namespace values from the individual.
 
+[0.6.1]:                       https://github.com/OpenBEL/openbel-api/compare/0.6.0...0.6.1
+[0.6.0]:                       https://github.com/OpenBEL/openbel-api/compare/0.5.1...0.6.0
 [0.5.1]:                       https://github.com/OpenBEL/openbel-api/compare/0.5.0...0.5.1
 [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
+[44]:                          https://github.com/OpenBEL/openbel-api/issues/44
 [91]:                          https://github.com/OpenBEL/openbel-api/issues/91
 [92]:                          https://github.com/OpenBEL/openbel-api/issues/92
 [93]:                          https://github.com/OpenBEL/openbel-api/issues/93
+[95]:                          https://github.com/OpenBEL/openbel-api/issues/95
+[99]:                          https://github.com/OpenBEL/openbel-api/issues/99
+[102]:                         https://github.com/OpenBEL/openbel-api/issues/102

data/README.md

@@ -54,7 +54,7 @@ The OpenBEL API is built to run with [JRuby][JRuby] and [Java 8][Java 8].
 - [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
+- [MongoDB][MongoDB], version 3.2 or greater
   - Follow [MongoDB download][MongoDB download] page for download and installation instructions.
 - [SQLite][SQLite], version 3.8.0 or greater
   - Follow [SQLite download][SQLite download] page for download and installation instructions. 
@@ -236,7 +236,7 @@ API documentation with *Try it* functionality is available [here][OpenBEL API do
 
 -----
 
-Built with collaboration and :heart: by the [OpenBEL][OpenBEL] community.
+Built with collaboration and a lot of :heart: by the [OpenBEL][OpenBEL] community.
 
 [OpenBEL]: http://www.openbel.org
 [OpenBEL Platform]: https://github.com/OpenBEL/openbel-platform

data/VERSION

@@ -1 +1 @@
-0.5.1
+0.6.1

data/app/openbel/api/config.rb

@@ -92,6 +92,18 @@ module OpenBEL
         ]
       end
 
+      # Check Mongo server version >= 3.2.
+      # The aggregation framework's $slice operator is used which requires 3.2.
+      if mongo_client.server_version.to_s !~ /^3.2/
+        return [
+          true, <<-ERR
+            MongoDB version 3.2 or greater is required.
+
+            MongoDB version: #{mongo_client.server_version}
+          ERR
+        ]
+      end
+
       # Attempt access of database.
       db = mongo_client.db(mongo[:database])
 

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

@@ -0,0 +1,17 @@
+module OpenBEL
+  module Helpers
+
+    DEFAULT_CONTENT_TYPE    = 'application/hal+json'
+    DEFAULT_CONTENT_TYPE_ID = :hal
+
+    def wants_default?
+      if params[:format]
+        return params[:format] == DEFAULT_CONTENT_TYPE
+      end
+
+      request.accept.any? { |accept_entry|
+        accept_entry.to_s == DEFAULT_CONTENT_TYPE
+      }
+    end
+  end
+end

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

@@ -0,0 +1,74 @@
+require          'bel/util'
+require_relative 'base'
+require_relative 'translators'
+
+module OpenBEL
+  module Helpers
+
+    def render_evidence_collection(
+      name, page_results, start, size, filters,
+      filtered_total, collection_total, evidence_api
+    )
+      # see if the user requested a BEL translator (Accept header or ?format)
+      translator        = Translators.requested_translator(request, params)
+      translator_plugin = Translators.requested_translator_plugin(request, params)
+
+      halt 404 unless page_results[:cursor].has_next?
+
+      # Serialize to HAL if they [Accept]ed it, specified it as ?format, or
+      # no translator was found to match request.
+      if wants_default? || !translator
+        facets   = page_results[:facets]
+        pager    = Pager.new(start, size, filtered_total)
+        evidence = page_results[:cursor].map { |item|
+                     item.delete('facets')
+                     item
+                   }.to_a
+
+        options = {
+          :facets   => facets,
+          :start    => start,
+          :size     => size,
+          :filters  => filters,
+          :metadata => {
+            :collection_paging => {
+              :total                  => collection_total,
+              :total_filtered         => pager.total_size,
+              :total_pages            => pager.total_pages,
+              :current_page           => pager.current_page,
+              :current_page_size      => evidence.size,
+            }
+          }
+        }
+
+        # pager links
+        options[:previous_page] = pager.previous_page
+        options[:next_page]     = pager.next_page
+
+        render_collection(evidence, :evidence, options)
+      else
+        extension = translator_plugin.file_extensions.first
+
+        response.headers['Content-Type'] = translator_plugin.media_types.first
+        status 200
+        attachment "#{name}.#{extension}"
+        stream :keep_open do |response|
+          cursor             = page_results[:cursor]
+          dataset_evidence = cursor.lazy.map { |evidence|
+            evidence.delete('facets')
+            evidence.delete('_id')
+            evidence = BEL::Model::Evidence.create(BEL.keys_to_symbols(evidence))
+            evidence.bel_statement = BEL::Model::Evidence.parse_statement(evidence)
+            evidence
+          }
+
+          translator.write(
+            dataset_evidence, response,
+            :annotation_reference_map => evidence_api.find_all_annotation_references,
+            :namespace_reference_map  => evidence_api.find_all_namespace_references
+          )
+        end
+      end
+    end
+  end
+end

data/app/openbel/api/helpers/filters.rb

@@ -0,0 +1,94 @@
+module OpenBEL
+  module Helpers
+
+    # Parse filter query parameters and partition into an {Array}. The first
+    # index will contain the valid filters and the second index will contain
+    # the invalid filters.
+    #
+    # @param [Array<String>] filter_query_params an array of filter strings
+    #        encoded in JSON
+    # @return [Array<Array<Hash>, Array<String>] the first index holds the
+    #         valid, filter {Hash hashes}; the second index holds the invalid,
+    #         filter {String strings}
+    def parse_filters(filter_query_params)
+      filter_query_params.map { |filter_string|
+        begin
+          MultiJson.load filter_string
+        rescue MultiJson::ParseError => ex
+          "#{ex} (filter: #{filter_string})"
+        end
+      }.partition { |filter|
+        filter.is_a?(Hash)
+      }
+    end
+
+    # Retrieve the filters that do not provide category, name, and value keys.
+    #
+    # The parsed, incomplete filters will contain an +:error+ key that provides
+    # an error message intended for the user.
+    #
+    # @param [Array<Hash>] filters an array of filter {Hash hashes}
+    # @return [Array<Hash>] an array of incomplete filter {Hash hashes} that
+    #         contain a human-readable error at the +:error+ key
+    def incomplete_filters(filters)
+      filters.select { |filter|
+        ['category', 'name', 'value'].any? { |f| !filter.include? f }
+      }.map { |incomplete_filter|
+        category, name, value = incomplete_filter.values_at('category', 'name', 'value')
+        error = <<-MSG.gsub(/^\s+/, '').strip
+          Incomplete filter, category:"#{category}", name:"#{name}", and value:"#{value}".
+        MSG
+        incomplete_filter.merge(:error => error)
+      }
+    end
+
+    # Retrieve the filters that represent invalid full-text search values.
+    #
+    # The parsed, invalid full-text search filters will contain an +:error+ key
+    # that provides an error message intended for the user.
+    #
+    # @param [Array<Hash>] filters an array of filter {Hash hashes}
+    # @return [Array<Hash>] an array of invalid full-text search filter
+    #         {Hash hashes} that contain a human-readable error at the
+    #         +:error+ key
+    def invalid_fts_filters(filters)
+      filters.select { |filter|
+        category, name, value = filter.values_at('category', 'name', 'value')
+        category == 'fts' && name == 'search' && value.to_s.length <= 1
+      }.map { |invalid_fts_filter|
+        error = <<-MSG.gsub(/^\s+/, '').strip
+          Full-text search filter values must be larger than one.
+        MSG
+        invalid_fts_filter.merge(:error => error)
+      }
+    end
+
+    # Validate the requested filter query strings. If all filters are valid
+    # then return them as {Hash hashes}, otherwise halt 400 Bad Request and
+    # return JSON error response.
+    def validate_filters!
+      filter_query_params = CGI::parse(env["QUERY_STRING"])['filter']
+      valid_filters, invalid_filters = parse_filters(filter_query_params)
+
+      invalid_filters |= incomplete_filters(valid_filters)
+      invalid_filters |= invalid_fts_filters(valid_filters)
+
+      return valid_filters if invalid_filters.empty?
+
+      halt(400, { 'Content-Type' => 'application/json' }, render_json({
+        :status => 400,
+        :msg => "Bad Request",
+        :detail =>
+          invalid_filters.
+          map { |invalid_filter|
+            if invalid_filter.is_a?(Hash) && invalid_filter[:error]
+              invalid_filter[:error]
+            else
+              invalid_filter
+            end
+          }.
+          map(&:to_s)
+      }))
+    end
+  end
+end

data/app/openbel/api/helpers/translators.rb

@@ -0,0 +1,73 @@
+require 'bel'
+
+module OpenBEL
+  module Helpers
+
+    # Helpers for translator functionality based on user's requested media
+    # type.
+    module Translators
+
+      # Open {::Sinatra::Helpers::Stream} and add the +puts+, +write+, and
+      # +flush+ methods. This is necessary because the RDF.rb writers will call
+      # these methods on the IO (in this case {::Sinatra::Helpers::Stream}).
+      class ::Sinatra::Helpers::Stream
+
+        # Write each string in +args*, new-line delimited, to the stream.
+        def puts(*args)
+          self << (
+            args.map { |string| "#{string.encode(Encoding::UTF_8)}\n" }.join
+          )
+        end
+
+        # Write the string to the stream.
+        def write(string)
+          self << string.encode(Encoding::UTF_8)
+        end
+
+        # flush is a no-op; flushing is handled by sinatra/rack server
+        def flush; end
+      end
+
+      # Find a bel.rb translator plugin by value. The value is commonly the
+      # id, file extension, or media type associated with the translator
+      # plugin.
+      #
+      # @param  [#to_s] value     used to look up translator plugin registered
+      #        with bel.rb
+      # @return [BEL::Translator] the translator instance; or +nil+ if one
+      #         cannot be found
+      def self.for(value)
+        BEL.translator(symbolize_value(value))
+      end
+
+      def self.plugin_for(value)
+        BEL::Translator::Plugins.for(symbolize_value(value))
+      end
+
+      def self.requested_translator_plugin(request, params)
+        if params && params[:format]
+          self.plugin_for(params[:format])
+        else
+          request.accept.flat_map { |accept_entry|
+            self.plugin_for(accept_entry)
+          }.compact.first
+        end
+      end
+
+      def self.requested_translator(request, params)
+        if params && params[:format]
+          self.for(params[:format])
+        else
+          request.accept.flat_map { |accept_entry|
+            self.for(accept_entry)
+          }.compact.first
+        end
+      end
+
+      def self.symbolize_value(value)
+        value.to_s.to_sym
+      end
+      private_class_method :symbolize_value
+    end
+  end
+end

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

@@ -94,23 +94,11 @@ module OpenBEL
 
         def free_annotation(name, value)
           {
-            :name  => normalize_annotation_name(name),
+            :name  => name,
             :value => value
           }
         end
 
-        def normalize_annotation_name(name, options = {})
-          name_s = name.to_s
-
-          if name_s.empty?
-            nil
-          else
-            name_s.
-              split(%r{[^a-zA-Z0-9]+}).
-              map! { |word| word.capitalize }.
-              join
-          end
-        end
       end
 
       class AnnotationGroupingTransform