Merge pull request #152 from ncbo/develop

Develop to master merge, release v5.31.0
ontoportal-lirmm · Jun 12, 2024 · 8910ca4 · 8910ca4
2 parents f39d91d + 4c35bb9
commit 8910ca4
Show file tree

Hide file tree

Showing 33 changed files with 6,455 additions and 620 deletions.
diff --git a/Gemfile b/Gemfile
@@ -40,13 +40,15 @@ gem 'unicorn-worker-killer'
 gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
 gem 'redcarpet'
 
-# NCBO
-gem 'goo', github: 'ncbo/goo', branch: 'master'
-gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master'
-gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'master'
-gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'master'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+
+# NCBO gems (can be from a local dev path or from rubygems/git)
+gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop'
+gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'develop'
+gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'develop'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
+gem 'goo', github: 'ncbo/goo', branch: 'develop'
+gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop'
+
 
 group :development do
   # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42
@@ -74,4 +76,5 @@ group :test do
   gem 'rack-test'
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io
+  gem 'webmock', '~> 3.19.1'
 end
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: ef2d816df2d263c905bd034efd449a964fa4890f
-  branch: master
+  revision: 70007faf43d0d96292809f89f15a27a757ccaa25
+  branch: develop
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -16,8 +16,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: 63c986880aa88c9384043e6611a682434a14aba7
-  branch: master
+  revision: 7531e10ad55ac66e925c099d7fc05a5a3ceae67e
+  branch: develop
   specs:
     ncbo_annotator (0.0.1)
       goo
@@ -27,11 +27,13 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: f239b34230131cd7cfb9eec5b34068ba990b698b
-  branch: master
+  revision: 89b68775fca3ab7d6451171bc3fee7679a82a1d5
+  branch: develop
   specs:
     ncbo_cron (0.0.1)
       dante
+      faraday (~> 2)
+      faraday-follow_redirects (~> 0)
       goo
       google-analytics-data
       mlanett-redis-lock
@@ -43,8 +45,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: 013abea4af3b10910ec661dbb358a4b6cae198a4
-  branch: master
+  revision: f92a42f660635522eb8709e618ff2e641aef0d17
+  branch: develop
   specs:
     ncbo_ontology_recommender (0.0.1)
       goo
@@ -54,8 +56,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 02986ff6db698cd56fdc062fed21b65d706a9598
-  branch: master
+  revision: 013a322440b4cfd899908d15ff605799acf8e6ef
+  branch: develop
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -74,8 +76,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc
-  branch: master
+  revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc
+  branch: develop
   specs:
     sparql-client (1.0.1)
       json_pure (>= 1.4)
@@ -112,7 +114,9 @@ GEM
     backports (3.25.0)
     base64 (0.2.0)
     bcrypt (3.1.20)
-    bcrypt_pbkdf (1.1.0)
+    bcrypt_pbkdf (1.1.1)
+    bcrypt_pbkdf (1.1.1-arm64-darwin)
+    bcrypt_pbkdf (1.1.1-x86_64-darwin)
     bigdecimal (1.4.2)
     builder (3.2.4)
     capistrano (3.18.1)
@@ -130,6 +134,9 @@ GEM
     coderay (1.1.3)
     concurrent-ruby (1.2.3)
     connection_pool (2.4.1)
+    crack (1.0.0)
+      bigdecimal
+      rexml
     cube-ruby (0.0.3)
     dante (0.2.0)
     date (3.3.4)
@@ -140,6 +147,8 @@ GEM
       base64
       faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
+    faraday-follow_redirects (0.3.0)
+      faraday (>= 1, < 3)
     faraday-net_http (3.0.2)
     faraday-retry (2.2.1)
       faraday (~> 2.0)
@@ -198,6 +207,7 @@ GEM
     haml (5.2.2)
       temple (>= 0.8.0)
       tilt
+    hashdiff (1.1.0)
     http-accept (1.7.0)
     http-cookie (1.0.5)
       domain_name (~> 0.5)
@@ -223,7 +233,7 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0305)
+    mime-types-data (3.2024.0507)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-stub_any_instance (1.0.3)
@@ -232,7 +242,7 @@ GEM
     multi_json (1.15.0)
     mutex_m (0.2.0)
     net-http-persistent (2.9.4)
-    net-imap (0.4.10)
+    net-imap (0.4.11)
       date
       net-protocol
     net-pop (0.1.2)
@@ -263,7 +273,7 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.0.5)
-    racc (1.7.3)
+    racc (1.8.0)
     rack (1.6.13)
     rack-accept (0.4.5)
       rack (>= 0.4)
@@ -279,7 +289,7 @@ GEM
       rack
     rack-test (2.1.0)
       rack (>= 1.3)
-    rack-timeout (0.6.3)
+    rack-timeout (0.7.0)
     rainbow (3.1.1)
     raindrops (0.20.1)
     rake (10.5.0)
@@ -288,26 +298,27 @@ GEM
     redcarpet (3.6.0)
     redis (5.2.0)
       redis-client (>= 0.22.0)
-    redis-client (0.22.1)
+    redis-client (0.22.2)
       connection_pool
     redis-rack-cache (2.2.1)
       rack-cache (>= 1.10, < 2)
       redis-store (>= 1.6, < 2)
     redis-store (1.10.0)
       redis (>= 4, < 6)
-    regexp_parser (2.9.0)
+    regexp_parser (2.9.2)
     request_store (1.7.0)
       rack (>= 1.4)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.2.6)
+    rexml (3.2.8)
+      strscan (>= 3.0.9)
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.63.4)
+    rubocop (1.63.5)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -359,6 +370,7 @@ GEM
       net-scp (>= 1.1.2)
       net-sftp (>= 2.1.2)
       net-ssh (>= 2.8.0)
+    strscan (3.1.0)
     systemu (2.6.5)
     temple (0.10.3)
     tilt (2.3.0)
@@ -374,13 +386,16 @@ GEM
       unicorn (>= 4, < 7)
     uuid (2.3.9)
       macaddr (~> 1.0)
+    webmock (3.19.1)
+      addressable (>= 2.8.0)
+      crack (>= 0.3.2)
+      hashdiff (>= 0.4.0, < 2.0.0)
 
 PLATFORMS
   aarch64-linux
   arm64-darwin-22
   arm64-darwin-23
   x86_64-darwin-18
-  x86_64-darwin-21
   x86_64-darwin-23
   x86_64-linux
 
@@ -432,6 +447,7 @@ DEPENDENCIES
   sparql-client!
   unicorn
   unicorn-worker-killer
+  webmock (~> 3.19.1)
 
 BUNDLED WITH
    2.4.22
diff --git a/app.rb b/app.rb
@@ -27,13 +27,16 @@
 require_relative 'lib/rack/cube_reporter'
 require_relative 'lib/rack/param_translator'
 require_relative 'lib/rack/slice_detection'
+require_relative 'lib/rack/request_lang'
 
 # Logging setup
 require_relative "config/logging"
 
 # Inflector setup
 require_relative "config/inflections"
 
+require 'request_store'
+
 # Protection settings
 set :protection, :except => :path_traversal
 
@@ -141,6 +144,9 @@
 use Rack::PostBodyToParams
 use Rack::ParamTranslator
 
+use RequestStore::Middleware
+use Rack::RequestLang
+
 use LinkedData::Security::Authorization
 use LinkedData::Security::AccessDenied
 

diff --git a/config/solr/property_search/enumsconfig.xml b/config/solr/property_search/enumsconfig.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" ?>
+<enumsConfig>
+  <enum name="ontologyType">
+    <value>ONTOLOGY</value>
+    <value>VALUE_SET_COLLECTION</value>
+  </enum>
+  <enum name="propertyType">
+    <value>ANNOTATION</value>
+    <value>DATATYPE</value>
+    <value>OBJECT</value>
+  </enum>
+</enumsConfig>