Develop to Master merge, release v6.2.0

Gemfile.lock

@@ -56,7 +56,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: f614b4feb4361eaa4fb13289139fd029a2622872
+  revision: 93e0844e19c3632bbd613a3e33869e267a6f2e25
   branch: master
   specs:
     ontologies_linked_data (0.0.1)
@@ -119,7 +119,7 @@ GEM
     bcrypt (3.1.20)
     bcrypt_pbkdf (1.1.1)
     bcrypt_pbkdf (1.1.1-arm64-darwin)
-    bigdecimal (3.1.9)
+    bigdecimal (3.2.2)
     builder (3.3.0)
     capistrano (3.19.2)
       airbrussh (>= 1.0.0)
@@ -150,7 +150,7 @@ GEM
       logger
     faraday-follow_redirects (0.3.0)
       faraday (>= 1, < 3)
-    faraday-net_http (3.4.0)
+    faraday-net_http (3.4.1)
       net-http (>= 0.5.0)
     faraday-retry (2.3.1)
       faraday (~> 2.0)
@@ -218,15 +218,15 @@ GEM
       domain_name (~> 0.5)
     i18n (1.14.7)
       concurrent-ruby (~> 1.0)
-    json (2.11.3)
+    json (2.12.2)
     json-schema (2.8.1)
       addressable (>= 2.4)
     json_pure (2.8.1)
     jwt (2.10.1)
       base64
     kgio (2.11.4)
     language_server-protocol (3.17.0.4)
-    libxml-ruby (5.0.3)
+    libxml-ruby (5.0.4)
     lint_roller (1.1.0)
     logger (1.7.0)
     macaddr (1.7.2)
@@ -237,10 +237,10 @@ GEM
       net-pop
       net-smtp
     method_source (1.1.0)
-    mime-types (3.6.2)
+    mime-types (3.7.0)
       logger
-      mime-types-data (~> 3.2015)
-    mime-types-data (3.2025.0429)
+      mime-types-data (~> 3.2025, >= 3.2025.0507)
+    mime-types-data (3.2025.0701)
     mini_mime (1.1.5)
     minitest (5.25.5)
     minitest-hooks (1.5.2)
@@ -255,7 +255,7 @@ GEM
     net-http (0.6.0)
       uri
     net-http-persistent (2.9.4)
-    net-imap (0.5.8)
+    net-imap (0.5.9)
       date
       net-protocol
     net-pop (0.1.2)
@@ -271,13 +271,13 @@ GEM
     net-ssh (7.3.0)
     netrc (0.11.0)
     newrelic_rpm (9.18.0)
-    oj (3.16.10)
+    oj (3.16.11)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
-    ostruct (0.6.1)
+    ostruct (0.6.2)
     parallel (1.27.0)
     parseconfig (1.1.2)
     parser (3.3.8.0)
@@ -315,7 +315,7 @@ GEM
     redcarpet (3.6.1)
     redis (5.4.0)
       redis-client (>= 0.22.0)
-    redis-client (0.24.0)
+    redis-client (0.25.0)
       connection_pool
     redis-rack-cache (2.2.1)
       rack-cache (>= 1.10, < 2)

config/unicorn.rb

@@ -68,11 +68,11 @@
   # Unicorn master loads the app then forks off workers - because of the way
   # Unix forking works, we need to make sure we aren't using any of the parent's
   # sockets, e.g. db connection
+  #
+  # the following is highly recomended for Rails + "preload_app true"
+  # as there's no need for the master process to hold a connection
+  defined?(ActiveRecord::Base) and ActiveRecord::Base.connection.disconnect!
 
   # Redis and Memcached would go here but their connections are established
   # on demand, so the master never opens a socket
 end
-
-if settings.enable_unicorn_workerkiller && defined?(Unicorn)
-  require_relative './config/unicorn_workerkiller'
-end

controllers/submission_metadata_controller.rb

@@ -1,14 +1,37 @@
 class SubmissionMetadataController < ApplicationController
-
   ##
   # Display all metadata for submissions
   get '/submission_metadata' do
     reply klass_metadata(LinkedData::Models::OntologySubmission, 'submission_metadata')
   end
 
+  ##
+  # Display metadata for a specific submission attribute
+  get '/submission_metadata/:attribute' do
+    attribute = params[:attribute]
+    metadata = klass_metadata(LinkedData::Models::OntologySubmission, 'submission_metadata')
+    attribute_metadata = metadata.find { |attr| attr[:attribute] == attribute }
+
+    halt 404, "Metadata for attribute '#{attribute}' not found" unless attribute_metadata
+
+    reply attribute_metadata
+  end
+
   ##
   # Display all metadata for ontologies
   get '/ontology_metadata' do
     reply klass_metadata(LinkedData::Models::Ontology, 'ontology_metadata')
   end
-end
+
+  ##
+  # Display metadata for a specific ontology attribute
+  get '/ontology_metadata/:attribute' do
+    attribute = params[:attribute]
+    metadata = klass_metadata(LinkedData::Models::Ontology, 'ontology_metadata')
+    attribute_metadata = metadata.find { |attr| attr[:attribute] == attribute }
+
+    halt 404, "Metadata for attribute '#{attribute}' not found" unless attribute_metadata
+
+    reply attribute_metadata
+  end
+end

test/controllers/test_properties_controller.rb

@@ -35,7 +35,7 @@ def test_properties
     get "/ontologies/#{@@acronyms.first}/properties"
     assert last_response.ok?
     results = MultiJson.load(last_response.body)
-    assert_equal 84, results.length
+    assert_equal 85, results.length
 
     get "/ontologies/#{@@acronyms.last}/properties"
     assert last_response.ok?
@@ -59,7 +59,7 @@ def test_property_roots
     get "/ontologies/#{@@acronyms.first}/properties/roots"
     assert last_response.ok?
     pr = MultiJson.load(last_response.body)
-    assert_equal 61, pr.length
+    assert_equal 62, pr.length
 
     # count object properties
     opr = pr.select { |p| p["@type"] == "http://www.w3.org/2002/07/owl#ObjectProperty" }
@@ -69,7 +69,7 @@ def test_property_roots
     assert_equal 32, dpr.length
     # count annotation properties
     apr = pr.select { |p| p["@type"] == "http://www.w3.org/2002/07/owl#AnnotationProperty" }
-    assert_equal 11, apr.length
+    assert_equal 12, apr.length
     # check for non-root properties
     assert_empty pr.select { |p| ["http://www.w3.org/2004/02/skos/core#broaderTransitive",
                                   "http://www.w3.org/2004/02/skos/core#topConceptOf",
@@ -103,7 +103,7 @@ def test_property_tree
     get "/ontologies/#{@@acronyms.first}/properties/http%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore%23topConceptOf/tree"
     assert last_response.ok?
     pr = MultiJson.load(last_response.body)
-    assert_equal 61, pr.length
+    assert_equal 62, pr.length
     num_found = 0
 
     pr.each do |p|