openbel-api 0.4.0-java

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

@@ -0,0 +1,41 @@
+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

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

@@ -0,0 +1,382 @@
+require 'bel'
+require 'cgi'
+require 'multi_json'
+require 'uri'
+
+module OpenBEL
+  module Routes
+
+    # REST API for retrieving namespaces and values.  Provides the following capabilities:
+    #
+    # * Retrieve namespaces.
+    # * Retrieve values for a namespace using the identifier, preferred name, or title.
+    # * Retrieve equivalences for one or more values.
+    # * Retrieve equivalences in a target namespace for one or more values.
+    # * Retrieve orthologs for one or more values.
+    # * Retrieve orthologs in a target namespace for one or more values.
+    class Namespaces < Base
+
+      RESULT_TYPES = {
+        :resource => :all,
+        :name => :prefLabel,
+        :identifier => :identifier,
+        :title => :title
+      }
+
+      def initialize(app)
+        super
+
+        # RdfRepository using Jena.
+        @rr = BEL::RdfRepository.plugins[:jena].create_repository(
+          :tdb_directory => OpenBEL::Settings[:resource_rdf][:jena][:tdb_directory]
+        )
+
+        # Namespaces using RdfRepository
+        @namespaces = BEL::Resource::Namespaces.new(@rr)
+
+        # Resource Search using SQLite.
+        @search = BEL::Resource::Search.plugins[:sqlite].create_search(
+          :database_file => OpenBEL::Settings[:resource_search][:sqlite][:database_file]
+        )
+      end
+
+      options '/api/namespaces' do
+        response.headers['Allow'] = 'OPTIONS,GET'
+        status 200
+      end
+
+      options '/api/namespaces/:namespace' do
+        response.headers['Allow'] = 'OPTIONS,GET'
+        status 200
+      end
+
+      options '/api/namespaces/:namespace/equivalents' do
+        response.headers['Allow'] = 'OPTIONS,POST,GET'
+        status 200
+      end
+
+      options '/api/namespaces/:namespace/orthologs' do
+        response.headers['Allow'] = 'OPTIONS,POST,GET'
+        status 200
+      end
+
+      options '/api/namespaces/:namespace/values/:value' do
+        response.headers['Allow'] = 'OPTIONS,GET'
+        status 200
+      end
+
+      options '/api/namespaces/:namespace/values/:value/equivalents' do
+        response.headers['Allow'] = 'OPTIONS,GET'
+        status 200
+      end
+
+      options '/api/namespaces/:namespace/values/:value/equivalents/:target' do
+        response.headers['Allow'] = 'OPTIONS,GET'
+        status 200
+      end
+
+      options '/api/namespaces/:namespace/values/:value/orthologs' do
+        response.headers['Allow'] = 'OPTIONS,GET'
+        status 200
+      end
+
+      options '/api/namespaces/:namespace/values/:value/orthologs/:target' do
+        response.headers['Allow'] = 'OPTIONS,GET'
+        status 200
+      end
+
+      get '/api/namespaces' do
+        namespaces = @namespaces.each.to_a
+
+        halt 404 if not namespaces or namespaces.empty?
+
+        render_collection(
+          namespaces.sort { |x,y|
+            x.prefLabel.to_s <=> y.prefLabel.to_s
+          },
+          :namespace
+        )
+      end
+
+      get '/api/namespaces/values' do
+        start    = (params[:start]  ||  0).to_i
+        size     = (params[:size]   || -1).to_i
+        size     = -1 if size <= 0
+        faceted  = as_bool(params[:faceted])
+        halt 501 if faceted
+
+        filter_hash = Hash.new{ |h,k| h[k] = Hash.new(&h.default_proc) }
+        filter_params = CGI::parse(env["QUERY_STRING"])['filter']
+        filter_params.each do |filter|
+          filter = read_filter(filter)
+          halt 400 unless ['category', 'name', 'value'].all? { |f| filter.include? f}
+          filter_hash[filter['category']][filter['name']] = filter['value']
+        end
+
+        halt 404 unless filter_hash['fts']['search'].is_a?(String)
+        match = filter_hash['fts']['search']
+        halt 404 unless match.length > 1
+
+        match_results = @search.search(wildcard_match(match), :namespace_concept, nil, nil,
+          :start => start,
+          :size => size
+        ).map { |result|
+          value = OpenBEL::Resource::Namespaces::NamespaceValueSearchResult.new(@rr, result.uri)
+          value.match_text = result.snippet
+          value
+        }.to_a
+
+        halt 404 if not match_results or match_results.empty?
+        render_collection(
+          match_results,
+          :namespace_value,
+          :adapter => Oat::Adapters::BasicJson
+        )
+      end
+
+      get '/api/namespaces/:namespace' do |namespace|
+        namespace = @namespaces.find(namespace).first
+
+        halt 404 unless namespace
+
+        status 200
+        render_resource(
+          namespace,
+          :namespace
+        )
+      end
+
+      get '/api/namespaces/:namespace/values' do |namespace|
+        namespace = @namespaces.find(namespace).first
+        halt 404 unless namespace
+
+        start    = (params[:start]  ||  0).to_i
+        size     = (params[:size]   || -1).to_i
+        size     = -1 if size <= 0
+        faceted  = as_bool(params[:faceted])
+        halt 501 if faceted
+
+        filter_hash = Hash.new{ |h,k| h[k] = Hash.new(&h.default_proc) }
+        filter_params = CGI::parse(env["QUERY_STRING"])['filter']
+        filter_params.each do |filter|
+          filter = read_filter(filter)
+          halt 400 unless ['category', 'name', 'value'].all? { |f| filter.include? f}
+          filter_hash[filter['category']][filter['name']] = filter['value']
+        end
+
+        halt 404 unless filter_hash['fts']['search'].is_a?(String)
+        match = filter_hash['fts']['search']
+        halt 404 unless match.length > 1
+
+        match_results = @search.search(wildcard_match(match), :namespace_concept, namespace.uri.to_s, nil,
+          :start => start,
+          :size => size
+        ).map { |result|
+          value = OpenBEL::Resource::Namespaces::NamespaceValueSearchResult.new(@rr, result.uri)
+          value.match_text = result.snippet
+          value
+        }.to_a
+
+        halt 404 if not match_results or match_results.empty?
+        render_collection(
+          match_results,
+          :namespace_value,
+          :adapter => Oat::Adapters::BasicJson
+        )
+      end
+
+      # TODO Requires a Namespace API to retrieve equivalents for matched values.
+      # get '/api/namespaces/:namespace/equivalents' do |namespace|
+      #   halt 400 unless request.params['value']
+
+      #   values = CGI::parse(env["QUERY_STRING"])['value']
+      #   options = {}
+      #   if request.params['namespace']
+      #     options[:target] = request.params['namespace']
+      #   end
+
+      #   if request.params['result']
+      #     result = request.params['result'].to_sym
+      #     halt 400 unless RESULT_TYPES.include? result
+      #     options[:result] = RESULT_TYPES[result]
+      #   end
+
+      #   eq_mapping = @api.find_equivalents(namespace, values, options)
+      #   halt 404 if eq_mapping.values.all? { |v| v == nil }
+      #   response.headers['Content-Type'] = 'application/json'
+      #   MultiJson.dump eq_mapping
+      # end
+
+      # TODO Requires a Namespace API to retrieve equivalents for matched values.
+      # post '/api/namespaces/:namespace/equivalents' do |namespace|
+      #   halt 400 unless request.media_type == 'application/x-www-form-urlencoded'
+
+      #   content = request.body.read
+      #   halt 400 if content.empty?
+
+      #   params = Hash[
+      #     URI.decode_www_form(content).group_by(&:first).map{
+      #       |k,a| [k,a.map(&:last)]
+      #     }
+      #   ]
+
+      #   halt 400 unless params['value']
+
+      #   options = {}
+      #   if params['namespace']
+      #     options[:target] = params['namespace'].first
+      #   end
+
+      #   if params['result']
+      #     result = params['result'].first.to_sym
+      #     halt 400 unless RESULT_TYPES.include? result
+      #     options[:result] = RESULT_TYPES[result]
+      #   end
+
+      #   eq_mapping = @api.find_equivalents(namespace, params['value'], options)
+      #   response.headers['Content-Type'] = 'application/json'
+      #   MultiJson.dump eq_mapping
+      # end
+
+      # TODO Requires a Namespace API to retrieve orthologs for matched values.
+      # get '/api/namespaces/:namespace/orthologs' do |namespace|
+      #   halt 400 unless request.params['value']
+
+      #   values = CGI::parse(env["QUERY_STRING"])['value']
+      #   options = {}
+      #   if request.params['namespace']
+      #     options[:target] = request.params['namespace']
+      #   end
+
+      #   if request.params['result']
+      #     result = request.params['result'].to_sym
+      #     halt 400 unless RESULT_TYPES.include? result
+      #     options[:result] = RESULT_TYPES[result]
+      #   end
+
+      #   orth_mapping = @api.find_orthologs(namespace, values, options)
+      #   halt 404 if orth_mapping.values.all? { |v| v == nil }
+      #   response.headers['Content-Type'] = 'application/json'
+      #   MultiJson.dump orth_mapping
+      # end
+
+      # TODO Requires a Namespace API to retrieve orthologs for matched values.
+      # post '/api/namespaces/:namespace/orthologs' do |namespace|
+      #   halt 400 unless request.media_type == 'application/x-www-form-urlencoded'
+
+      #   content = request.body.read
+      #   halt 400 if content.empty?
+
+      #   params = Hash[
+      #     URI.decode_www_form(content).group_by(&:first).map{
+      #       |k,a| [k,a.map(&:last)]
+      #     }
+      #   ]
+
+      #   halt 400 unless params['value']
+
+      #   options = {}
+      #   if params['namespace']
+      #     options[:target] = params['namespace'].first
+      #   end
+
+      #   if params['result']
+      #     result = params['result'].first.to_sym
+      #     halt 400 unless RESULT_TYPES.include? result
+      #     options[:result] = RESULT_TYPES[result]
+      #   end
+
+      #   orth_mapping = @api.find_orthologs(namespace, params['value'], options)
+      #   response.headers['Content-Type'] = 'application/json'
+      #   MultiJson.dump orth_mapping
+      # end
+
+      get '/api/namespaces/:namespace/values/:value' do |namespace, value|
+        namespace = @namespaces.find(namespace).first
+        halt 404 unless namespace
+
+        value = namespace.find(value).first
+        halt 404 unless value
+
+        status 200
+        render_resource(
+          value,
+          :namespace_value,
+          :adapter => Oat::Adapters::BasicJson
+        )
+      end
+
+      get '/api/namespaces/:namespace/values/:value/equivalents' do |namespace, value|
+        namespace = @namespaces.find(namespace).first
+        halt 404 unless namespace
+
+        value = namespace.find(value).first
+        halt 404 unless value
+
+        equivalents = value.equivalents.to_a
+        halt 404 if not equivalents or equivalents.empty?
+
+        render_collection(
+          equivalents,
+          :namespace_value,
+          :adapter => Oat::Adapters::BasicJson
+        )
+      end
+
+      get '/api/namespaces/:namespace/values/:value/equivalents/:target' do |namespace, value, target|
+        namespace = @namespaces.find(namespace).first
+        halt 404 unless namespace
+        halt 404 unless @namespaces.find(target).first
+
+        value = namespace.find(value).first
+        halt 404 unless value
+
+        target_equivalents = value.equivalents(target).to_a
+        halt 404 if not target_equivalents or target_equivalents.empty?
+
+        render_collection(
+          target_equivalents,
+          :namespace_value,
+          :adapter => Oat::Adapters::BasicJson
+        )
+      end
+
+      get '/api/namespaces/:namespace/values/:value/orthologs' do |namespace, value|
+        namespace = @namespaces.find(namespace).first
+        halt 404 unless namespace
+
+        value = namespace.find(value).first
+        halt 404 unless value
+
+        orthologs = value.orthologs.to_a
+        halt 404 if not orthologs or orthologs.empty?
+
+        render_collection(
+          orthologs,
+          :namespace_value,
+          :adapter => Oat::Adapters::BasicJson
+        )
+      end
+
+      get '/api/namespaces/:namespace/values/:value/orthologs/:target' do |namespace, value, target|
+        namespace = @namespaces.find(namespace).first
+        halt 404 unless namespace
+        halt 404 unless @namespaces.find(target).first
+
+        value = namespace.find(value).first
+        halt 404 unless value
+
+        target_orthologs = value.orthologs(target).to_a
+        halt 404 if not target_orthologs or target_orthologs.empty?
+
+        render_collection(
+          target_orthologs,
+          :namespace_value,
+          :adapter => Oat::Adapters::BasicJson
+        )
+      end
+    end
+  end
+end
+# vim: ts=2 sw=2:
+# encoding: utf-8

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

@@ -0,0 +1,39 @@
+module OpenBEL
+  module Routes
+
+    class Root < Base
+
+      options '/api' do
+        response.headers['Allow'] = 'OPTIONS,GET'
+        status 200
+      end
+
+      get '/api' do
+        response.headers['Content-Type'] = 'application/hal+json'
+        MultiJson.dump({
+          :_links => {
+            :item => [
+              {
+                :href => "#{base_url}/api/annotations"
+              },
+              {
+                :href => "#{base_url}/api/evidence"
+              },
+              {
+                :href => "#{base_url}/api/expressions"
+              },
+              {
+                :href => "#{base_url}/api/functions"
+              },
+              {
+                :href => "#{base_url}/api/namespaces"
+              }
+            ]
+          }
+        })
+      end
+    end
+  end
+end
+# vim: ts=2 sw=2:
+# encoding: utf-8