Merge branch 'master' into development

ontoportal-lirmm · Jun 26, 2024 · 310ae5f · 310ae5f
2 parents ad6c578 + a90b97c
commit 310ae5f
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diff --git a/.github/workflows/docker-image.yml b/.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 }}
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -29,7 +29,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 0855adfce5365c6ef7a494e3d3ad9af2611974d9
+  revision: a5b56a68e6dc8ecfc9db708d44350342dac38ce6
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -74,19 +74,22 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    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)
+    activesupport (4.0.13)
+      i18n (~> 0.6, >= 0.6.9)
+      minitest (~> 4.2)
+      multi_json (~> 1.3)
+      thread_safe (~> 0.1)
+      tzinfo (~> 0.3.37)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
     base64 (0.2.0)
     bcrypt (3.1.20)
     bigdecimal (3.1.8)
     binding_of_caller (1.0.1)
       debug_inspector (>= 1.2.0)
-    builder (3.2.4)
+    builder (3.3.0)
     coderay (1.1.3)
-    concurrent-ruby (1.2.3)
+    concurrent-ruby (1.3.3)
     connection_pool (2.4.1)
     cube-ruby (0.0.3)
     dante (0.2.0)
@@ -136,30 +139,34 @@ GEM
     google-cloud-env (2.1.1)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.4.0)
+    google-protobuf (3.25.3)
     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)
+    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)
+    googleapis-common-protos-types (1.15.0)
+      google-protobuf (>= 3.18, < 5.a)
     googleauth (1.11.0)
       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 (1.63.0-x86_64-darwin)
+    grpc (1.64.0)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.63.0-x86_64-linux)
+    grpc (1.64.0-x86_64-darwin)
+      google-protobuf (~> 3.25)
+      googleapis-common-protos-types (~> 1.0)
+    grpc (1.64.0-x86_64-linux)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
     htmlentities (4.3.4)
     http-accept (1.7.0)
-    http-cookie (1.0.5)
+    http-cookie (1.0.6)
       domain_name (~> 0.5)
     httpclient (2.8.3)
     i18n (0.9.5)
@@ -173,7 +180,7 @@ GEM
       multi_json (~> 1.15)
       rack (>= 2.2, < 4)
       rdf (~> 3.2, >= 3.2.10)
-    jwt (2.8.1)
+    jwt (2.8.2)
       base64
     launchy (2.5.2)
       addressable (~> 2.8)
@@ -187,7 +194,7 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0507)
+    mime-types-data (3.2024.0604)
     mini_mime (1.1.5)
     minitest (4.7.5)
     mlanett-redis-lock (0.2.7)
@@ -196,20 +203,20 @@ GEM
     net-http-persistent (4.0.2)
       connection_pool (~> 2.2)
     netrc (0.11.0)
-    oj (3.16.3)
+    oj (3.16.4)
       bigdecimal (>= 3.0)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
-    parallel (1.24.0)
+    parallel (1.25.1)
     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 (3.1.4)
     rack-test (2.1.0)
       rack (>= 1.3)
     rake (13.2.1)
@@ -244,8 +251,8 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     retriable (3.1.2)
-    rexml (3.2.8)
-      strscan (>= 3.0.9)
+    rexml (3.3.1)
+      strscan
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -274,14 +281,15 @@ GEM
     systemu (2.6.5)
     test-unit-minitest (0.9.1)
       minitest (~> 4.7)
+    thread_safe (0.3.6)
     trailblazer-option (0.1.2)
-    tzinfo (2.0.6)
-      concurrent-ruby (~> 1.0)
+    tzinfo (0.3.62)
     uber (0.1.0)
     uuid (2.3.9)
       macaddr (~> 1.0)
 
 PLATFORMS
+  ruby
   x86_64-darwin-23
   x86_64-linux
 

diff --git a/bin/ncbo_ontology_import b/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