Merge to Master: Release 2.1.1 - Migration tools and Archiving old su…

…bmission files (#16)

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* update Gemfile to set gem branch's development

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* add option force re-archiving  to archive_old_submissions script

* add request_store gem

* remove the ontology deletion in the test_parse_submissions to re-use it

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* add agroportal new model migration script

* [ontoportal-bot] Gemfile.lock update

* fix the attribute of type String migration  to URI didn't want to update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* update AgroPortal migration script  to handle values xsd:DataType

---------

Co-authored-by: OntoPortal Bot <[email protected]>

.github/workflows/ruby-unit-tests.yml

@@ -8,12 +8,12 @@ jobs:
   test:
     strategy:
       matrix:
-        backend: ['ruby', 'ruby-agraph'] # ruby runs tests with 4store backend and ruby-agraph runs with AllegroGraph backend
+        backend: ['ruby'] # ruby runs tests with 4store backend and ruby-agraph runs with AllegroGraph backend
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
     - name: copy config.rb file from template
-      run:  cp config/config.test.rb config/config.rb
+      run:  cp config/config.rb.sample config/config.rb
     - name: Build docker-compose
       working-directory: ./test
       run: docker-compose build

Gemfile

@@ -16,13 +16,14 @@ gem 'rake'
 gem 'redis'
 gem 'rest-client'
 gem 'sys-proctable'
+gem 'request_store'
 
 # Monitoring
 gem 'cube-ruby', require: 'cube'
 
-gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'master'
+gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'master'
-gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'master'
+gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'development'
 gem 'ncbo_annotator', github: 'ontoportal-lirmm/ncbo_annotator', branch: 'master'
 # Testing
 group :test do
@@ -32,3 +33,4 @@ group :test do
   gem 'test-unit-minitest'
 end
 
+gem "binding_of_caller", "~> 1.0"

Gemfile.lock

@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: e47cf0442d5be0c8a811f591c98e93cf3e0af5fc
-  branch: master
+  revision: 9aa0ccacc9d76bff096218e6d48edc5b0bffd54f
+  branch: development
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -26,8 +26,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: b1d8504f434d3821b967fa07cbe17f7f3d286b41
-  branch: master
+  revision: 1cfaf4482b7bf8c9001f0ff309f2a0ff06f683b5
+  branch: development
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -74,19 +74,21 @@ GEM
     activesupport (3.2.22.5)
       i18n (~> 0.6, >= 0.6.4)
       multi_json (~> 1.0)
-    addressable (2.8.1)
+    addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
-    bcrypt (3.1.18)
+    bcrypt (3.1.20)
+    binding_of_caller (1.0.0)
+      debug_inspector (>= 0.0.1)
     builder (3.2.4)
     coderay (1.1.3)
-    concurrent-ruby (1.1.10)
-    connection_pool (2.3.0)
+    concurrent-ruby (1.2.2)
+    connection_pool (2.4.1)
     cube-ruby (0.0.3)
     dante (0.2.0)
+    debug_inspector (1.1.0)
     declarative (0.0.20)
     docile (1.4.0)
-    domain_name (0.5.20190701)
-      unf (>= 0.0.5, < 1.0.0)
+    domain_name (0.6.20231109)
     email_spec (2.1.1)
       htmlentities (~> 4.3.3)
       launchy (~> 2.1)
@@ -114,10 +116,10 @@ GEM
     faraday-patron (1.0.0)
     faraday-rack (1.0.0)
     faraday-retry (1.0.3)
-    ffi (1.15.5)
-    google-apis-analytics_v3 (0.12.0)
-      google-apis-core (>= 0.9.1, < 2.a)
-    google-apis-core (0.9.5)
+    ffi (1.16.3)
+    google-apis-analytics_v3 (0.13.0)
+      google-apis-core (>= 0.11.0, < 2.a)
+    google-apis-core (0.11.2)
       addressable (~> 2.5, >= 2.5.1)
       googleauth (>= 0.16.2, < 2.a)
       httpclient (>= 2.8.1, < 3.a)
@@ -126,10 +128,12 @@ GEM
       retriable (>= 2.0, < 4.a)
       rexml
       webrick
-    googleauth (1.3.0)
-      faraday (>= 0.17.3, < 3.a)
+    google-cloud-env (2.0.1)
+      faraday (>= 1.0, < 3.a)
+    googleauth (1.9.0)
+      faraday (>= 1.0, < 3.a)
+      google-cloud-env (~> 2.0, >= 2.0.1)
       jwt (>= 1.4, < 3.0)
-      memoist (~> 0.16)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
@@ -140,28 +144,27 @@ GEM
     httpclient (2.8.3)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.6.3)
-    json_pure (2.6.3)
-    jwt (2.6.0)
+    json (2.7.1)
+    json_pure (2.7.1)
+    jwt (2.7.1)
     launchy (2.5.2)
       addressable (~> 2.8)
-    libxml-ruby (4.0.0)
-    logger (1.5.3)
+    libxml-ruby (4.1.2)
+    logger (1.6.0)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.6.6)
       mime-types (>= 1.16, < 4)
-    memoist (0.16.2)
     method_source (1.0.0)
-    mime-types (3.4.1)
+    mime-types (3.5.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2022.0105)
-    mini_mime (1.1.2)
+    mime-types-data (3.2023.1205)
+    mini_mime (1.1.5)
     minitest (4.7.5)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
-    multipart-post (2.2.3)
+    multipart-post (2.3.0)
     net-http-persistent (2.9.4)
     netrc (0.11.0)
     oj (2.18.5)
@@ -174,28 +177,30 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.1)
-    rack (3.0.4.1)
-    rack-test (2.0.2)
+    public_suffix (5.0.4)
+    rack (3.0.8)
+    rack-test (2.1.0)
       rack (>= 1.3)
-    rake (13.0.6)
+    rake (13.1.0)
     rdf (1.0.8)
       addressable (>= 2.2)
-    redis (5.0.6)
-      redis-client (>= 0.9.0)
-    redis-client (0.12.1)
+    redis (5.0.8)
+      redis-client (>= 0.17.0)
+    redis-client (0.19.0)
       connection_pool
     representable (3.2.0)
       declarative (< 0.1.0)
       trailblazer-option (>= 0.1.1, < 0.2.0)
       uber (< 0.2.0)
+    request_store (1.5.1)
+      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)
     retriable (3.1.2)
-    rexml (3.2.5)
+    rexml (3.2.6)
     rsolr (2.5.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -204,7 +209,7 @@ GEM
     rubyzip (2.3.2)
     rufus-scheduler (2.0.24)
       tzinfo (>= 0.3.22)
-    signet (0.17.0)
+    signet (0.18.0)
       addressable (~> 2.8)
       faraday (>= 0.17.5, < 3.a)
       jwt (>= 1.5, < 3.0)
@@ -224,20 +229,19 @@ GEM
     test-unit-minitest (0.9.1)
       minitest (~> 4.7)
     trailblazer-option (0.1.2)
-    tzinfo (2.0.5)
+    tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     uber (0.1.0)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.8.2)
     uuid (2.3.9)
       macaddr (~> 1.0)
-    webrick (1.7.0)
+    webrick (1.8.1)
 
 PLATFORMS
+  x86_64-darwin-23
   x86_64-linux
 
 DEPENDENCIES
+  binding_of_caller (~> 1.0)
   cube-ruby
   email_spec
   faraday (~> 1.9)
@@ -256,6 +260,7 @@ DEPENDENCIES
   pry
   rake
   redis
+  request_store
   rest-client
   simplecov
   simplecov-cobertura
@@ -264,4 +269,4 @@ DEPENDENCIES
   test-unit-minitest
 
 BUNDLED WITH
-   2.3.23
+   2.4.21