openbel-api 1.2.4-java → 1.2.5-java

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: b69d590f8e724877211c8a7d3bb68e636f9ffefa
+  metadata.gz: 90c37f3793684521d80dc8295c45455fe6dfb451
+  data.tar.gz: 5f045dbece8c755bdf1d5d83be7c5252c9ef1e2e
 SHA512:
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+  data.tar.gz: ccce717ee6f5b560c00bf9fa77ec1da3748c3f240a3fdde32e784815d4b76aaa1818f0ff2d84525625b34efdcafe280c7b871a52f31995937868760262554e1c

data/VERSION

@@ -1 +1 @@
-1.2.4
+1.2.5

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

@@ -103,7 +103,8 @@ module OpenBEL
         private
 
         def setup(item)
-          @annotation_id, @annotation_value_id = URI(item.uri).path.split('/')[3..-1]
+          @annotation_id       = item.annotation.prefix.first
+          @annotation_value_id = item.identifier.first
         end
 
         def link_self

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

@@ -103,24 +103,23 @@ module OpenBEL
       class NamespaceValueResourceSerializer < BaseSerializer
         adapter Oat::Adapters::HAL
         schema do
-          parts = URI(item.delete(:rdf_uri)).path.split('/')[3..-1]
-          namespace_id = parts[0]
-          namespace_value_id = parts.join('/')
+          id       = item[:namespace][:prefix]
+          value_id = item[:identifier]
 
           type     :namespace_value
           property :namespace_value, item
-          link     :self,            link_self(namespace_value_id)
-          link     :collection,      link_namespace(namespace_id)
-          link     :equivalents,     link_equivalents(namespace_value_id)
-          link     :orthologs,       link_orthologs(namespace_value_id)
+          link     :self,            link_self(id, value_id)
+          link     :collection,      link_namespace(id)
+          link     :equivalents,     link_equivalents(id, value_id)
+          link     :orthologs,       link_orthologs(id, value_id)
         end
 
         private
 
-        def link_self(id)
+        def link_self(id, value_id)
           {
             :type => :namespace_value,
-            :href => "#{base_url}/api/namespaces/#{id}"
+            :href => "#{base_url}/api/namespaces/#{id}/values/#{value_id}"
           }
         end
 
@@ -131,17 +130,17 @@ module OpenBEL
           }
         end
 
-        def link_equivalents(id)
+        def link_equivalents(id, value_id)
           {
             :type => :namespace_value_collection,
-            :href => "#{base_url}/api/namespaces/#{id}/equivalents"
+            :href => "#{base_url}/api/namespaces/#{id}/values/#{value_id}/equivalents"
           }
         end
 
-        def link_orthologs(id)
+        def link_orthologs(id, value_id)
           {
             :type => :namespace_value_collection,
-            :href => "#{base_url}/api/namespaces/#{id}/orthologs"
+            :href => "#{base_url}/api/namespaces/#{id}/values/#{value_id}/orthologs"
           }
         end
       end

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

@@ -285,11 +285,14 @@ module OpenBEL
             {'Content-Type' => 'application/json'},
             render_json(
               {
-                valid_syntax:    false,
-                valid_semantics: false,
-                message:         'Invalid syntax.',
-                warnings:        [],
-                term_signatures: []
+                validation: {
+                  expression:      bel,
+                  valid_syntax:    false,
+                  valid_semantics: false,
+                  message:         'Invalid syntax.',
+                  warnings:        [],
+                  term_signatures: []
+                }
               }
             )
           )

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: openbel-api
 version: !ruby/object:Gem::Version
-  version: 1.2.4
+  version: 1.2.5
 platform: java
 authors:
 - Anthony Bargnesi