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ncbo · May 5, 2024 · 1d35da7 · 1d35da7
1 parent de8d191
commit 1d35da7
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Showing 11 changed files with 620 additions and 875 deletions.
diff --git a/.gitignore b/.gitignore
@@ -16,6 +16,7 @@ logs/**
 .tags*
 cache/**
 vendor/bundle/*
+ontologies_api.iml
 
 # YARD artifacts
 .yardoc
@@ -31,7 +32,7 @@ bin/**
 
 # Support local configs
 config/environments/*
-!config/environments/config.rb
+!config/environments/development.rb.sample
 !config/environments/config.rb.sample
 
 #ignore capistrano deployment
@@ -57,7 +58,7 @@ test/data/ontology_files/repo/**/*
 
 config/environments/console.rb
 
-config/environments/stage.rb
+config/environments/development.rb.sample
 
 config/environments/benchmark.rb
 
@@ -68,3 +69,5 @@ test/data/ontology_files/catalog-v001.xml
 create_permissions.log
 
 ontologies_api.iml
+
+.env
diff --git a/Gemfile b/Gemfile
@@ -48,9 +48,9 @@ gem 'redcarpet'
 gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'development'
 gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'master'
 gem 'ncbo_ontology_recommender', git: 'https://github.com/ncbo/ncbo_ontology_recommender.git', branch: 'master'
-gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
-gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'development'
-gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'development'
+gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'pr/sync-agroportal-bioportal'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'pr/sync-agroportal-ncbo'
 
 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

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
-  remote: https://github.com/ncbo/goo.git
-  revision: f01386fe55ffba39cbf5e0bf95c8e2dc18767711
+  remote: https://github.com/ncbo/ncbo_ontology_recommender.git
+  revision: 013abea4af3b10910ec661dbb358a4b6cae198a4
   branch: master
   specs:
     ncbo_ontology_recommender (0.0.1)
@@ -9,28 +9,36 @@ GIT
       ontologies_linked_data
       redis
 
+GIT
+  remote: https://github.com/ncbo/sparql-client.git
+  revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc
+  branch: master
+  specs:
+    sparql-client (1.0.1)
+      json_pure (>= 1.4)
+      net-http-persistent (= 2.9.4)
+      rdf (>= 1.0)
+
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: b2a635fb1e8206e6e3010be4dbe033b47eb58481
-  branch: development
+  revision: f2751fe9324e48a0a5c2a8b15580ab879fc53a2b
+  branch: pr/sync-agroportal-bioportal
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
       pry
-      rdf (= 3.2.11)
-      rdf-raptor
-      rdf-rdfxml
-      rdf-vocab
+      rdf (= 1.0.8)
       redis
+      request_store
       rest-client
       rsolr
       sparql-client
       uuid
 
 GIT
-  remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: 63c986880aa88c9384043e6611a682434a14aba7
-  branch: master
+  remote: https://github.com/ontoportal-lirmm/ncbo_annotator.git
+  revision: 1eb751b65d10ae23d45c74e0516c78754a8419f0
+  branch: development
   specs:
     ncbo_annotator (0.0.1)
       goo
@@ -39,14 +47,15 @@ GIT
       ruby-xxHash
 
 GIT
-  remote: https://github.com/ncbo/ncbo_cron.git
-  revision: b5764cc314758dbfdbb855b2b63c1c53b1325f6f
+  remote: https://github.com/ontoportal-lirmm/ncbo_cron.git
+  revision: 9ec0147203007cc368a5119ffe1a019fa8701c14
   branch: master
   specs:
     ncbo_cron (0.0.1)
       dante
       goo
       google-analytics-data
+      google-apis-analytics_v3
       mlanett-redis-lock
       multi_json
       ncbo_annotator
@@ -55,20 +64,9 @@ GIT
       rufus-scheduler (~> 2.0.24)
 
 GIT
-  remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: 013abea4af3b10910ec661dbb358a4b6cae198a4
-  branch: master
-  specs:
-    ncbo_ontology_recommender (0.0.1)
-      goo
-      ncbo_annotator
-      ontologies_linked_data
-      redis
-
-GIT
-  remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 4dc3b1123e871b53ba9eb51983ff69c5d2c75c18
-  branch: master
+  remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
+  revision: f70abe981c6fb3533b7785d58b7234855bcd5cf2
+  branch: pr/sync-agroportal-ncbo
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -85,15 +83,6 @@ GIT
       rsolr
       rubyzip
 
-GIT
-  remote: https://github.com/ncbo/sparql-client.git
-  revision: d418d56a6c9ff5692f925b45739a2a1c66bca851
-  branch: master
-  specs:
-    sparql-client (3.2.2)
-      net-http-persistent (~> 4.0, >= 4.0.2)
-      rdf (~> 3.2, >= 3.2.11)
-
 GIT
   remote: https://github.com/palexander/rack-post-body-to-params.git
   revision: 0fd30e710386d0cb8a3a6833d9549d7b655d5398
@@ -118,7 +107,7 @@ GEM
       multi_json (~> 1.0)
     addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
-    airbrussh (1.5.1)
+    airbrussh (1.5.2)
       sshkit (>= 1.6.1, != 1.7.0)
     ast (2.4.2)
     backports (3.25.0)
@@ -142,9 +131,13 @@ 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)
+    declarative (0.0.20)
     docile (1.4.0)
     domain_name (0.6.20240107)
     ed25519 (1.3.0)
@@ -153,7 +146,7 @@ GEM
       faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
     faraday-net_http (3.0.2)
-    faraday-retry (2.2.0)
+    faraday-retry (2.2.1)
       faraday (~> 2.0)
     ffi (1.16.3)
     gapic-common (0.21.1)
@@ -172,13 +165,22 @@ GEM
     google-analytics-data-v1beta (0.12.0)
       gapic-common (>= 0.21.1, < 2.a)
       google-cloud-errors (~> 1.0)
+    google-apis-analytics_v3 (0.15.0)
+      google-apis-core (>= 0.14.0, < 2.a)
+    google-apis-core (0.14.1)
+      addressable (~> 2.5, >= 2.5.1)
+      googleauth (~> 1.9)
+      httpclient (>= 2.8.1, < 3.a)
+      mini_mime (~> 1.0)
+      representable (~> 3.0)
+      retriable (>= 2.0, < 4.a)
+      rexml
     google-cloud-core (1.7.0)
       google-cloud-env (>= 1.0, < 3.a)
       google-cloud-errors (~> 1.0)
     google-cloud-env (2.1.1)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.4.0)
-    google-protobuf (3.25.3-aarch64-linux)
     google-protobuf (3.25.3-arm64-darwin)
     google-protobuf (3.25.3-x86_64-darwin)
     google-protobuf (3.25.3-x86_64-linux)
@@ -195,32 +197,31 @@ GEM
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.62.0-aarch64-linux)
-      google-protobuf (~> 3.25)
-      googleapis-common-protos-types (~> 1.0)
-    grpc (1.62.0-arm64-darwin)
+    grpc (1.63.0-arm64-darwin)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.62.0-x86_64-darwin)
+    grpc (1.63.0-x86_64-darwin)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.62.0-x86_64-linux)
+    grpc (1.63.0-x86_64-linux)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
     haml (5.2.2)
       temple (>= 0.8.0)
       tilt
     hashdiff (1.1.0)
-    htmlentities (4.3.4)
     http-accept (1.7.0)
     http-cookie (1.0.5)
       domain_name (~> 0.5)
+    httpclient (2.8.3)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.7.1)
+    json (2.7.2)
+    json-ld (1.1.1)
+      rdf (>= 1.0.8)
     json-schema (2.8.1)
       addressable (>= 2.4)
-    json_pure (2.7.1)
+    json_pure (2.7.2)
     jwt (2.8.1)
       base64
     kgio (2.11.4)
@@ -234,7 +235,7 @@ GEM
       net-imap
       net-pop
       net-smtp
-    method_source (1.0.0)
+    method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
     mime-types-data (3.2024.0305)
@@ -259,24 +260,24 @@ GEM
       net-ssh (>= 5.0.0, < 8.0.0)
     net-smtp (0.5.0)
       net-protocol
-    net-ssh (7.2.1)
+    net-ssh (7.2.3)
     netrc (0.11.0)
-    newrelic_rpm (9.8.0)
+    newrelic_rpm (9.9.0)
     oj (3.16.1)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
     parallel (1.24.0)
     parseconfig (1.1.2)
-    parser (3.3.0.5)
+    parser (3.3.1.0)
       ast (~> 2.4.1)
       racc
     pony (1.13.1)
       mail (>= 2.0)
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.4)
+    public_suffix (5.0.5)
     racc (1.7.3)
     rack (1.6.13)
     rack-accept (0.4.5)
@@ -300,26 +301,33 @@ GEM
     rdf (1.0.8)
       addressable (>= 2.2)
     redcarpet (3.6.0)
-    redis (5.1.0)
-      redis-client (>= 0.17.0)
-    redis-client (0.21.1)
+    redis (5.2.0)
+      redis-client (>= 0.22.0)
+    redis-client (0.22.1)
       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)
+    representable (3.2.0)
+      declarative (< 0.1.0)
+      trailblazer-option (>= 0.1.1, < 0.2.0)
+      uber (< 0.2.0)
+    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)
+    retriable (3.1.2)
     rexml (3.2.6)
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.62.1)
+    rubocop (1.63.4)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -330,8 +338,8 @@ GEM
       rubocop-ast (>= 1.31.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.31.2)
-      parser (>= 3.3.0.4)
+    rubocop-ast (1.31.3)
+      parser (>= 3.3.1.0)
     ruby-progressbar (1.13.0)
     ruby-xxHash (0.4.0.2)
     ruby2_keywords (0.0.5)
@@ -365,7 +373,8 @@ GEM
       rack-test
       sinatra (~> 1.4.0)
       tilt (>= 1.3, < 3)
-    sshkit (1.22.0)
+    sshkit (1.22.2)
+      base64
       mutex_m
       net-scp (>= 1.1.2)
       net-sftp (>= 2.1.2)
@@ -374,8 +383,10 @@ GEM
     temple (0.10.3)
     tilt (2.3.0)
     timeout (0.4.1)
+    trailblazer-option (0.1.2)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
+    uber (0.1.0)
     unicode-display_width (2.5.0)
     unicorn (6.1.0)
       kgio (~> 2.6)
@@ -385,13 +396,14 @@ 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
 
@@ -435,6 +447,7 @@ DEPENDENCIES
   redis
   redis-rack-cache (~> 2.0)
   redis-store (~> 1.10)
+  request_store
   rubocop
   shotgun!
   simplecov