diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml index 6105c1d8..8639cb53 100644 --- 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 @@ -19,16 +24,25 @@ 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 @@ -36,7 +50,7 @@ jobs: 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 index 60d92551..8c3e9a19 100644 --- a/Gemfile.lock +++ b/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) @@ -88,13 +88,13 @@ 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) @@ -102,13 +102,13 @@ GEM 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) diff --git a/bin/ncbo_ontology_import b/bin/ncbo_ontology_import index 73fa7fac..9e6bc543 100755 --- 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