Feature: Align to AgroPortal 3.0

.github/workflows/docker-image.yml

@@ -1,12 +1,17 @@
-name: Docker Image CI
+name: Docker branch Images build
 
 on:
+  push:
+    branches:
+      - master
+      - development
+      - stage
+      - test
   release:
-    types: [published]
-
+    types: [ published ]
 jobs:
   push_to_registry:
-    name: Push Docker image to Docker Hub
+    name: Push Docker branch image to Docker Hub
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
@@ -19,24 +24,33 @@ jobs:
         uses: docker/setup-buildx-action@v2
 
       - name: Log in to Docker Hub
-        uses: docker/login-action@v2
+        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
       - name: Extract metadata (tags, labels) for Docker
         id: meta
         uses: docker/metadata-action@v4
         with:
-          images: bioportal/ncbo_cron
+          images: |
+            agroportal/ncbo_cron
+            ghcr.io/${{ github.repository }}
 
       - name: Build and push Docker image
         uses: docker/build-push-action@v4
         with:
           context: .
           platforms: linux/amd64,linux/arm64
           build-args: |
-            RUBY_VERSION=2.7
+            RUBY_VERSION=2.7.8
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/lifewatch-eric/ontologies_linked_data.git
-  revision: 0b551acdd7460914b2e4ebfc25017e04db4abaa7
+  revision: 32ee5870e220b62678b8dd81e6f29087678b9446
   branch: master
   specs:
     ontologies_linked_data (0.0.1)
@@ -20,7 +20,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: b2a635fb1e8206e6e3010be4dbe033b47eb58481
+  revision: f8ac7b00e8d8b46d1eea04de014175525c1cdd83
   branch: development
   specs:
     goo (0.0.2)
@@ -77,9 +77,9 @@ GEM
     activesupport (3.2.22.5)
       i18n (~> 0.6, >= 0.6.4)
       multi_json (~> 1.0)
-    addressable (2.8.6)
-      public_suffix (>= 2.0.2, < 6.0)
-    airbrussh (1.5.2)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
+    airbrussh (1.5.3)
       sshkit (>= 1.6.1, != 1.7.0)
     base64 (0.2.0)
     bcrypt (3.1.20)
@@ -88,27 +88,27 @@ GEM
     bigdecimal (3.1.8)
     binding_of_caller (1.0.1)
       debug_inspector (>= 1.2.0)
-    builder (3.2.4)
-    capistrano (3.18.1)
+    builder (3.3.0)
+    capistrano (3.19.1)
       airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
       sshkit (>= 1.9.0)
-    capistrano-bundler (2.1.0)
+    capistrano-bundler (2.1.1)
       capistrano (~> 3.1)
     capistrano-locally (0.3.0)
       capistrano (~> 3.0)
     capistrano-rbenv (2.2.0)
       capistrano (~> 3.1)
       sshkit (~> 1.3)
     coderay (1.1.3)
-    concurrent-ruby (1.2.3)
+    concurrent-ruby (1.3.4)
     connection_pool (2.4.1)
     cube-ruby (0.0.3)
     dante (0.2.0)
     debug_inspector (1.2.0)
     declarative (0.0.20)
-    docile (1.4.0)
+    docile (1.4.1)
     domain_name (0.6.20240107)
     ed25519 (1.3.0)
     email_spec (2.1.1)
@@ -122,7 +122,7 @@ GEM
     faraday-net_http (3.0.2)
     faraday-retry (2.2.1)
       faraday (~> 2.0)
-    ffi (1.16.3)
+    ffi (1.17.0)
     gapic-common (0.21.1)
       faraday (>= 1.9, < 3.a)
       faraday-retry (>= 1.0, < 3.a)
@@ -131,57 +131,57 @@ GEM
       googleapis-common-protos-types (>= 1.11.0, < 2.a)
       googleauth (~> 1.9)
       grpc (~> 1.59)
-    google-analytics-data (0.6.0)
+    google-analytics-data (0.6.1)
       google-analytics-data-v1beta (>= 0.11, < 2.a)
       google-cloud-core (~> 1.6)
-    google-analytics-data-v1beta (0.12.0)
+    google-analytics-data-v1beta (0.13.1)
       gapic-common (>= 0.21.1, < 2.a)
       google-cloud-errors (~> 1.0)
     google-apis-analytics_v3 (0.16.0)
       google-apis-core (>= 0.15.0, < 2.a)
-    google-apis-core (0.15.0)
+    google-apis-core (0.15.1)
       addressable (~> 2.5, >= 2.5.1)
       googleauth (~> 1.9)
-      httpclient (>= 2.8.1, < 3.a)
+      httpclient (>= 2.8.3, < 3.a)
       mini_mime (~> 1.0)
+      mutex_m
       representable (~> 3.0)
       retriable (>= 2.0, < 4.a)
-      rexml
-    google-cloud-core (1.7.0)
+    google-cloud-core (1.7.1)
       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-x86_64-darwin)
-    google-protobuf (3.25.3-x86_64-linux)
-    googleapis-common-protos (1.5.0)
-      google-protobuf (~> 3.18)
+    google-protobuf (3.25.5-x86_64-darwin)
+    google-protobuf (3.25.5-x86_64-linux)
+    googleapis-common-protos (1.6.0)
+      google-protobuf (>= 3.18, < 5.a)
       googleapis-common-protos-types (~> 1.7)
       grpc (~> 1.41)
-    googleapis-common-protos-types (1.14.0)
-      google-protobuf (~> 3.18)
-    googleauth (1.11.0)
+    googleapis-common-protos-types (1.16.0)
+      google-protobuf (>= 3.18, < 5.a)
+    googleauth (1.11.2)
       faraday (>= 1.0, < 3.a)
       google-cloud-env (~> 2.1)
       jwt (>= 1.4, < 3.0)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.64.0-x86_64-darwin)
-      google-protobuf (~> 3.25)
+    grpc (1.65.2-x86_64-darwin)
+      google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.64.0-x86_64-linux)
-      google-protobuf (~> 3.25)
+    grpc (1.65.2-x86_64-linux)
+      google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
     htmlentities (4.3.4)
     http-accept (1.7.0)
-    http-cookie (1.0.5)
+    http-cookie (1.0.7)
       domain_name (~> 0.5)
     httpclient (2.8.3)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.7.2)
+    json (2.7.4)
     json-canonicalization (0.4.0)
     json-ld (3.2.5)
       htmlentities (~> 4.3)
@@ -190,49 +190,52 @@ GEM
       multi_json (~> 1.15)
       rack (>= 2.2, < 4)
       rdf (~> 3.2, >= 3.2.10)
-    jwt (2.8.1)
+    jwt (2.9.3)
       base64
     launchy (2.5.2)
       addressable (~> 2.8)
     libxml-ruby (5.0.3)
     link_header (0.0.8)
-    logger (1.6.0)
+    logger (1.6.1)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.6.6)
       mime-types (>= 1.16, < 4)
     method_source (1.1.0)
-    mime-types (3.5.2)
+    mime-types (3.6.0)
+      logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0507)
+    mime-types-data (3.2024.1001)
     mini_mime (1.1.5)
     minitest (4.7.5)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
     mutex_m (0.2.0)
-    net-http-persistent (4.0.2)
+    net-http-persistent (4.0.4)
       connection_pool (~> 2.2)
     net-scp (4.0.0)
       net-ssh (>= 2.6.5, < 8.0.0)
     net-sftp (4.0.0)
       net-ssh (>= 5.0.0, < 8.0.0)
-    net-ssh (7.2.3)
+    net-ssh (7.3.0)
     netrc (0.11.0)
-    oj (3.16.3)
+    oj (3.16.6)
       bigdecimal (>= 3.0)
+      ostruct (>= 0.2)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
-    parallel (1.24.0)
+    ostruct (0.6.0)
+    parallel (1.26.3)
     parseconfig (1.1.2)
     pony (1.13.1)
       mail (>= 2.0)
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.5)
-    rack (3.0.11)
+    public_suffix (5.1.1)
+    rack (3.1.8)
     rack-test (2.1.0)
       rack (>= 1.3)
     rake (13.2.1)
@@ -251,7 +254,7 @@ GEM
     rdf-xsd (3.2.1)
       rdf (~> 3.2)
       rexml (~> 3.2)
-    redis (5.2.0)
+    redis (5.3.0)
       redis-client (>= 0.22.0)
     redis-client (0.22.2)
       connection_pool
@@ -267,8 +270,7 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     retriable (3.1.2)
-    rexml (3.2.8)
-      strscan (>= 3.0.9)
+    rexml (3.3.9)
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -289,15 +291,14 @@ GEM
     simplecov-cobertura (2.1.0)
       rexml
       simplecov (~> 0.19)
-    simplecov-html (0.12.3)
+    simplecov-html (0.13.1)
     simplecov_json_formatter (0.1.4)
-    sshkit (1.22.2)
+    sshkit (1.23.2)
       base64
-      mutex_m
       net-scp (>= 1.1.2)
       net-sftp (>= 2.1.2)
       net-ssh (>= 2.8.0)
-    strscan (3.1.0)
+      ostruct
     sys-proctable (1.3.0)
       ffi (~> 1.1)
     systemu (2.6.5)

bin/ncbo_ontology_import

@@ -89,7 +89,7 @@ def create_ontology(ont_info)
     has_domains << category if category
   end
 
-  new_ontology.groups = groups
+  new_ontology.group = groups
   new_ontology.hasDomain = has_domains
   new_ontology
 end
@@ -106,6 +106,10 @@ def upload_submission(sub_info, ontology)
     sub_info['pullLocation'] = "#{sub_info['ontology']['links']['download']}?apikey=#{SOURCE_APIKEY}"
   end
 
+  if sub_info['URI'].blank?
+    sub_info['URI'] = "#{sub_info['id']}"
+  end
+
   # Build the json body
   # hasOntologyLanguage options: OWL, UMLS, SKOS, OBO
   # status: alpha, beta, production, retired