openbel-api 0.6.2-java → 1.0.0-java

data/app/openbel/api/middleware/auth.rb

@@ -4,7 +4,6 @@ require 'jwt'
 
 module OpenBEL
   module JWTMiddleware
-
     def self.encode(payload, secret)
       ::JWT.encode(payload, secret, 'HS256')
     end
@@ -13,35 +12,32 @@ module OpenBEL
       ::JWT.decode(token, secret, verify, options)
     end
 
-    def self.check_cookie(env)
+    def self.check_token(env)
       cookie_hdr = env['HTTP_COOKIE']
       auth_hdr = env['HTTP_AUTHORIZATION']
-      if cookie_hdr.nil? and auth_hdr.nil?
-        raise 'missing authorization cookie/header'
+      req = Rack::Request.new(env)
+      token_param = req.params['token']
+      if cookie_hdr.nil? && auth_hdr.nil? && token_param.nil?
+        raise 'missing authorization cookie, header, or parameter'
       end
 
-      if not cookie_hdr.nil?
+      unless cookie_hdr.nil?
         cookies = cookie_hdr.split('; ')
-        selected = cookies.select {|x| x.start_with?('jwt=') }
-        if selected.size > 0
+        selected = cookies.select { |x| x.start_with?('jwt=') }
+        unless selected.empty?
           tokens = selected[0].split('=')
-          if tokens.size > 1
-            token = tokens[1]
-          end
-        end
-        if token.nil?
-          raise 'malformed authorization cookie'
+          token = tokens[1] if tokens.size > 1
         end
       end
 
-      if not auth_hdr.nil?
+      unless auth_hdr.nil?
         tokens = auth_hdr.split('Bearer ')
-        if tokens.size != 2
-            raise 'malformed authorization header'
-        end
+        raise 'malformed authorization header' if tokens.size != 2
         token = tokens[1]
       end
 
+      token = token_param unless token_param.nil?
+
       secret = OpenBEL::Settings[:auth][:secret]
       secret = Base64.decode64(secret)
       # whether we should verify the token
@@ -52,6 +48,7 @@ module OpenBEL
       begin
         decoded_token = decode(token, secret, verify, options)
       rescue ::JWT::VerificationError => ve
+        puts ve.inspect
         raise 'invalid authorization token'
       rescue ::JWT::DecodeError => je
         puts je.inspect
@@ -62,35 +59,31 @@ module OpenBEL
 
       exp = env['jwt.payload']['exp']
       now = Time.now.to_i
-      if now > exp
-        raise 'token expired'
-      end
+      raise 'token expired' if now > exp
 
       env['email'] = env['jwt.payload']['email']
     end
 
     class Authentication
       def initialize(app, opts = {})
-        @app          = app
-        @paths       = opts.fetch(:paths, [])
+        @app = app
+        @paths = opts.fetch(:paths, [])
       end
 
       def call(env)
         check = false
-        if @paths.size == 0
+        if @paths.empty?
           # w/out paths, always check for token
           check = true
         else
           path = env['PATH_INFO']
           # w/ paths, only check for token iff matched
-          if @paths.any? {|x| path.start_with?(x)}
-            check = true
-          end
+          check = true if @paths.any? { |x| path.start_with?(x) }
         end
 
         if check
           begin
-            JWTMiddleware.check_cookie(env)
+            JWTMiddleware.check_token(env)
           rescue Exception => e
             return _401(e.message)
           end
@@ -101,8 +94,8 @@ module OpenBEL
       private
 
       def _401(message)
-        hdrs = {'Content-Type' => 'application/json'}
-        msg = {error: message }
+        hdrs = { 'Content-Type' => 'application/json' }
+        msg = { error: message }
         [401, hdrs, [msg.to_json]]
       end
     end

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

@@ -22,9 +22,9 @@ module OpenBEL
         schema do
           type     :annotation
           property :rdf_uri,    item.uri.to_s
-          property :name,       item.prefLabel
-          property :prefix,     item.prefix
-          property :domain,     item.domain
+          property :name,       item.pref_label.first
+          property :prefix,     item.prefix.first
+          property :domain,     item.domain.first
         end
       end
 
@@ -85,14 +85,14 @@ module OpenBEL
           type     :annotation_value
           property :rdf_uri,         item.uri.to_s
           property :type,            [item.type].flatten.map(&:to_s)
-          property :identifier,      item.identifier
-          property :name,            item.prefLabel
+          property :identifier,      item.identifier.first
+          property :name,            item.pref_label.first
           entity   :annotation,      item.annotation, AnnotationSerializer
 
           # Support inclusion of the matched text when annotation values are filtered by
           # a full-text search.
-          if item.match_text
-            property :match_text,    item.match_text
+          if item.respond_to?(:match_text) && item.match_text
+            property :match_text, item.match_text
           end
 
           setup(item)

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

@@ -11,11 +11,10 @@ module OpenBEL
         schema do
           type :function
           properties do |p|
-            p.short_form  item[:short_form]
-            p.long_form   item[:long_form]
-            p.description item[:description]
-            p.return_type item[:return_type]
-            p.signatures  item[:signatures]
+            p.short_form  item.short
+            p.long_form   item.long
+            p.description item.description
+            p.return_type item.return_type.to_sym
           end
         end
       end
@@ -26,12 +25,11 @@ module OpenBEL
         schema do
           type :function
           properties do |p|
-            p.functions      item
+            p.function      item
           end
 
-          link :self,        link_self(item.first[:short_form])
-          link :next,        link_next
-          link :collection,  link_collection
+          link :self,       link_self(item[:long_form])
+          link :collection, link_collection
         end
 
         private
@@ -45,53 +43,32 @@ module OpenBEL
 
         def link_collection
           {
-            :type => :'function_collection',
+            :type => :function_collection,
             :href => "#{base_url}/api/functions"
           }
         end
-
-        def link_next
-          fx_values = FUNCTIONS.values.uniq.sort_by { |fx|
-            fx[:short_form]
-          }
-          next_fx = fx_values[fx_values.index(item) + 1]
-          {
-            :type => :function,
-            :href => next_fx ?
-                       "#{base_url}/api/functions/#{next_fx[:short_form]}" :
-                       nil
-          }
-        end
       end
 
       class FunctionCollectionSerializer < BaseSerializer
         adapter Oat::Adapters::HAL
 
         schema do
-          type :'function_collection'
+          type :function_collection
           properties do |p|
-            p.functions      item
+            p.function_collection item
           end
 
-          link :self,       link_self
-          link :start,      link_start(item.first[:short_form])
+          link :self, link_self
         end
 
         private
 
         def link_self
           {
-            :type => :'function_collection',
+            :type => :function_collection,
             :href => "#{base_url}/api/functions"
           }
         end
-
-        def link_start(first_function)
-          {
-            :type => :function,
-            :href => "#{base_url}/api/functions/#{first_function}"
-          }
-        end
       end
     end
   end

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

@@ -22,9 +22,9 @@ module OpenBEL
         schema do
           type     :namespace
           property :rdf_uri, item.uri.to_s
-          property :name,    item.prefLabel
-          property :prefix,  item.prefix
-          property :domain,  item.domain
+          property :name,    item.pref_label.first
+          property :prefix,  item.prefix.first
+          property :domain,  item.domain.first
         end
       end
 
@@ -86,16 +86,16 @@ module OpenBEL
           type     :namespace_value
           property :rdf_uri,       item.uri.to_s
           property :type,          [item.type].flatten.map(&:to_s)
-          property :identifier,    item.identifier
-          property :name,          item.prefLabel
-          property :title,         item.title
-          property :species,       item.fromSpecies
+          property :identifier,    item.identifier.first
+          property :name,          item.pref_label.first
+          property :title,         item.title.first
+          property :species,       item.from_species.first
           entity   :namespace,     item.namespace, NamespaceSerializer
 
           # Support inclusion of the matched text when annotation values are filtered by
           # a full-text search.
-          if item.match_text
-            property :match_text,    item.match_text
+          if item.respond_to?(:match_text) && item.match_text
+            property :match_text, item.match_text
           end
         end
       end
@@ -160,10 +160,10 @@ module OpenBEL
           type :value_equivalence
           property :value,         item.value
           property :type,          item.type ? item.type.sub(VOCABULARY_RDF, '') : nil
-          property :identifier,    item.identifier
-          property :title,         item.title
-          property :species,       item.fromSpecies
-          property :namespace_uri, item.inScheme
+          property :identifier,    item.identifier.first
+          property :title,         item.title.first
+          property :species,       item.from_species.first
+          property :namespace_uri, item.in_scheme.first
 
           property :value_equivalence_collection, item.equivalences, NamespaceValueSerializer
         end

data/app/openbel/api/resources/{evidence.rb → nanopub.rb}

@@ -3,29 +3,29 @@ require_relative 'base'
 
 module OpenBEL
   module Resource
-    module Evidence
+    module Nanopub
 
-      class EvidenceSerializer < BaseSerializer
+      class NanopubSerializer < BaseSerializer
         adapter Oat::Adapters::HAL
 
         schema do
-          type :evidence
+          type :nanopub
           property :bel_statement,      item['bel_statement']
           property :citation,           item['citation']
-          property :summary_text,       item['summary_text']
+          property :support,       item['support']
           property :experiment_context, item['experiment_context']
           property :metadata,           item['metadata']
           property :id,                 item['_id']
         end
       end
 
-      class EvidenceResourceSerializer < BaseSerializer
+      class NanopubResourceSerializer < BaseSerializer
         adapter Oat::Adapters::HAL
 
         schema do
-          type :evidence
+          type :nanopub
           properties do |p|
-            p.evidence item
+            p.nanopub item
           end
 
           link :self,         link_self
@@ -38,25 +38,25 @@ module OpenBEL
           id = item[:id] || context[:_id]
           item.delete(:id)
           {
-            :type => :evidence,
-            :href => "#{base_url}/api/evidence/#{id}"
+            :type => :nanopub,
+            :href => "#{base_url}/api/nanopubs/#{id}"
           }
         end
 
         def link_collection
           {
-            :type => :evidence_collection,
-            :href => "#{base_url}/api/evidence"
+            :type => :nanopub_collection,
+            :href => "#{base_url}/api/nanopubs"
           }
         end
       end
 
-      class EvidenceCollectionSerializer < BaseSerializer
+      class NanopubCollectionSerializer < BaseSerializer
         adapter Oat::Adapters::HAL
 
         schema do
-          type     :evidence_collection
-          property :evidence_collection,   item
+          type     :nanopub_collection
+          property :nanopub_collection,   item
           property :facets,                context[:facets]
           property :metadata,              context[:metadata]
           link     :self,                  link_self
@@ -71,16 +71,16 @@ module OpenBEL
           start  = context[:start]
           size   = context[:size]
           {
-            :type => :evidence_collection,
-            :href => "#{base_url}/api/evidence?start=#{start}&size=#{size}&#{filter_query_params.join('&')}"
+            :type => :nanopub_collection,
+            :href => "#{base_url}/api/nanopubs?start=#{start}&size=#{size}&#{filter_query_params.join('&')}"
           }
         end
 
         def link_start
           size = context[:size]
           {
-            :type => :evidence_collection,
-            :href => "#{base_url}/api/evidence?start=0&size=#{size}&#{filter_query_params.join('&')}"
+            :type => :nanopub_collection,
+            :href => "#{base_url}/api/nanopubs?start=0&size=#{size}&#{filter_query_params.join('&')}"
           }
         end
 
@@ -89,8 +89,8 @@ module OpenBEL
           return {} unless previous_page
 
           {
-            :type => :evidence_collection,
-            :href => "#{base_url}/api/evidence?start=#{previous_page.start_offset}&size=#{previous_page.page_size}&#{filter_query_params.join('&')}"
+            :type => :nanopub_collection,
+            :href => "#{base_url}/api/nanopubs?start=#{previous_page.start_offset}&size=#{previous_page.page_size}&#{filter_query_params.join('&')}"
           }
         end
 
@@ -99,14 +99,14 @@ module OpenBEL
           return {} unless next_page
 
           {
-            :type => :evidence_collection,
-            :href => "#{base_url}/api/evidence?start=#{next_page.start_offset}&size=#{next_page.page_size}&#{filter_query_params.join('&')}"
+            :type => :nanopub_collection,
+            :href => "#{base_url}/api/nanopubs?start=#{next_page.start_offset}&size=#{next_page.page_size}&#{filter_query_params.join('&')}"
           }
         end
 
         def filter_query_params
           context[:filters].map { |filter|
-            "filter=#{filter}"
+            "filter=#{MultiJson.dump(filter)}"
           }
         end
       end

data/app/openbel/api/resources/{evidence_transform.rb → nanopub_transform.rb}

@@ -2,7 +2,7 @@ require 'bel'
 
 module OpenBEL
   module Resource
-    module Evidence
+    module Nanopub
 
       class AnnotationTransform
 
@@ -18,9 +18,9 @@ module OpenBEL
           @annotations = annotations
         end
 
-        def transform_evidence!(evidence, base_url)
-          if evidence
-            experiment_context = evidence.experiment_context
+        def transform_nanopub!(nanopub, base_url)
+          if nanopub
+            experiment_context = nanopub.experiment_context
             if experiment_context != nil
               experiment_context.values.map! { |annotation|
                 transform_annotation(annotation, base_url)
@@ -103,12 +103,12 @@ module OpenBEL
 
       class AnnotationGroupingTransform
 
-        ExperimentContext = ::BEL::Model::ExperimentContext
+        ExperimentContext = ::BEL::Nanopub::ExperimentContext
 
-        def transform_evidence!(evidence)
-          experiment_context = evidence.experiment_context
+        def transform_nanopub!(nanopub)
+          experiment_context = nanopub.experiment_context
           if experiment_context != nil
-            evidence.experiment_context = ExperimentContext.new(
+            nanopub.experiment_context = ExperimentContext.new(
               experiment_context.group_by { |annotation|
                 annotation[:name]
               }.values.map do |grouped_annotation|

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

@@ -0,0 +1,74 @@
+require 'bel'
+require_relative 'base'
+
+module OpenBEL
+  module Resource
+    module Relationships
+
+      class RelationshipSerializer < BaseSerializer
+        adapter Oat::Adapters::HAL
+
+        schema do
+          type :relationship
+          properties do |p|
+            p.short_form  item.short
+            p.long_form   item.long
+            p.description item.description
+          end
+        end
+      end
+
+      class RelationshipResourceSerializer < BaseSerializer
+        adapter Oat::Adapters::HAL
+
+        schema do
+          type :relationship
+          properties do |p|
+            p.relation      item
+          end
+
+          link :self,       link_self(item[:long_form])
+          link :collection, link_collection
+        end
+
+        private
+
+        def link_self(id)
+          {
+            :type => :relationship,
+            :href => "#{base_url}/api/relationships/#{id}"
+          }
+        end
+
+        def link_collection
+          {
+            :type => :relationship_collection,
+            :href => "#{base_url}/api/relationships"
+          }
+        end
+      end
+
+      class RelationshipCollectionSerializer < BaseSerializer
+        adapter Oat::Adapters::HAL
+
+        schema do
+          type :relationship_collection
+          properties do |p|
+            p.relationship_collection item
+          end
+
+          link :self, link_self
+        end
+
+        private
+
+        def link_self
+          {
+            :type => :relationship_collection,
+            :href => "#{base_url}/api/relationships"
+          }
+        end
+      end
+    end
+  end
+end