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Merge remote-tracking branch 'origin/development' into feature/ecopor…
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…tal/align-to-agroportal-3.0
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@syphax-bouazzouni
syphax-bouazzouni committed Oct 26, 2024
2 parents 2ff764e + 310ae5f commit 57b5865
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28 changes: 21 additions & 7 deletions .github/workflows/docker-image.yml
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Original file line number Diff line number Diff line change
@@ -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
Expand All @@ -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 }}
95 changes: 48 additions & 47 deletions Gemfile.lock
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Original file line number Diff line number Diff line change
@@ -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)
Expand All @@ -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)
Expand Down Expand Up @@ -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)
Expand All @@ -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)
Expand All @@ -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)
Expand All @@ -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)
Expand All @@ -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)
Expand All @@ -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
Expand All @@ -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)
Expand All @@ -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)
Expand Down
6 changes: 5 additions & 1 deletion bin/ncbo_ontology_import
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand Down

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