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Merge pull request #9 from ontoportal-lirmm/feature/extact-agroportal…
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…-model-to-ontoportal

Feature: Add all MOD metadata feilds to the submission object
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@alexskr
alexskr authored Feb 24, 2025
2 parents 1e4882b + 69cda4f commit cbb523b
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2 changes: 1 addition & 1 deletion .ruby-version
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3.0.6
3.1.0
4 changes: 1 addition & 3 deletions Dockerfile
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@@ -1,4 +1,4 @@
ARG RUBY_VERSION=3.0
ARG RUBY_VERSION=3.1
ARG DISTRO_NAME=bullseye

FROM ruby:$RUBY_VERSION-$DISTRO_NAME
Expand All @@ -14,8 +14,6 @@ COPY Gemfile* /srv/ontoportal/ontologies_api/

WORKDIR /srv/ontoportal/ontologies_api

RUN gem update --system
RUN gem install bundler
ENV BUNDLE_PATH=/srv/ontoportal/bundle
RUN bundle install

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4 changes: 3 additions & 1 deletion Gemfile
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Expand Up @@ -46,7 +46,7 @@ gem 'goo', github: 'ncbo/goo', branch: 'master'
gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master'
gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'master'
gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'master'
gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'feature/extract-agroportal-model-to-ontoportal'
gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'

group :development do
Expand Down Expand Up @@ -80,3 +80,5 @@ group :test do
gem 'webmock', '~> 3.19.1'
gem 'webrick'
end

gem 'net-ftp'
149 changes: 81 additions & 68 deletions Gemfile.lock
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Expand Up @@ -27,7 +27,7 @@ GIT

GIT
remote: https://github.com/ncbo/ncbo_cron.git
revision: 1e0cb7f5e230e1d19c02f11f3fd76ed9831a3807
revision: c703f1387bf633999a285938067a76a1bff3ec87
branch: master
specs:
ncbo_cron (0.0.1)
Expand Down Expand Up @@ -55,9 +55,19 @@ GIT
redis

GIT
remote: https://github.com/ncbo/ontologies_linked_data.git
revision: 536cbe5cef9e23abc299ed44942c0b3966f9c18d
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/ontologies_linked_data.git
revision: 0622986d71175da6eda30da3c222d7dea2fb3b46
branch: feature/extract-agroportal-model-to-ontoportal
specs:
ontologies_linked_data (0.0.1)
activesupport
Expand All @@ -74,16 +84,6 @@ GIT
rsolr
rubyzip

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/palexander/rack-post-body-to-params.git
revision: 0fd30e710386d0cb8a3a6833d9549d7b655d5398
Expand Down Expand Up @@ -118,7 +118,7 @@ GEM
bcrypt (3.1.20)
bcrypt_pbkdf (1.1.1)
bcrypt_pbkdf (1.1.1-arm64-darwin)
bigdecimal (3.1.8)
bigdecimal (3.1.9)
builder (3.3.0)
capistrano (3.19.2)
airbrussh (>= 1.0.0)
Expand All @@ -133,17 +133,17 @@ GEM
capistrano (~> 3.1)
sshkit (~> 1.3)
coderay (1.1.3)
concurrent-ruby (1.3.4)
connection_pool (2.4.1)
concurrent-ruby (1.3.5)
connection_pool (2.5.0)
crack (0.4.5)
rexml
cube-ruby (0.0.3)
dante (0.2.0)
date (3.4.0)
date (3.4.1)
docile (1.4.1)
domain_name (0.6.20240107)
ed25519 (1.3.0)
faraday (2.12.1)
faraday (2.12.2)
faraday-net_http (>= 2.0, < 3.5)
json
logger
Expand All @@ -153,75 +153,79 @@ GEM
net-http (>= 0.5.0)
faraday-retry (2.2.1)
faraday (~> 2.0)
ffi (1.17.0-aarch64-linux-gnu)
ffi (1.17.0-arm64-darwin)
ffi (1.17.0-x86_64-linux-gnu)
gapic-common (0.23.0)
ffi (1.17.1)
ffi (1.17.1-arm64-darwin)
gapic-common (0.25.0)
faraday (>= 1.9, < 3.a)
faraday-retry (>= 1.0, < 3.a)
google-cloud-env (~> 2.2)
google-logging-utils (~> 0.1)
google-protobuf (>= 3.25, < 5.a)
googleapis-common-protos (~> 1.6)
googleapis-common-protos-types (~> 1.15)
googleauth (~> 1.11)
grpc (~> 1.65)
googleauth (~> 1.12)
grpc (~> 1.66)
get_process_mem (0.2.7)
ffi (~> 1.0)
google-analytics-data (0.6.1)
google-analytics-data (0.7.0)
google-analytics-data-v1beta (>= 0.11, < 2.a)
google-cloud-core (~> 1.6)
google-analytics-data-v1beta (0.13.1)
gapic-common (>= 0.21.1, < 2.a)
google-analytics-data-v1beta (0.16.0)
gapic-common (>= 0.25.0, < 2.a)
google-cloud-errors (~> 1.0)
google-cloud-core (1.7.1)
google-cloud-env (>= 1.0, < 3.a)
google-cloud-errors (~> 1.0)
google-cloud-env (2.2.1)
faraday (>= 1.0, < 3.a)
google-cloud-errors (1.4.0)
google-protobuf (3.25.5-aarch64-linux)
google-protobuf (3.25.5-arm64-darwin)
google-protobuf (3.25.5-x86_64-linux)
google-logging-utils (0.1.0)
google-protobuf (3.25.6-aarch64-linux)
google-protobuf (3.25.6-arm64-darwin)
google-protobuf (3.25.6-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 (1.16.0)
googleapis-common-protos-types (1.18.0)
google-protobuf (>= 3.18, < 5.a)
googleauth (1.11.2)
googleauth (1.13.1)
faraday (>= 1.0, < 3.a)
google-cloud-env (~> 2.1)
google-cloud-env (~> 2.2)
google-logging-utils (~> 0.1)
jwt (>= 1.4, < 3.0)
multi_json (~> 1.11)
os (>= 0.9, < 2.0)
signet (>= 0.16, < 2.a)
grpc (1.67.0-aarch64-linux)
grpc (1.70.1-aarch64-linux)
google-protobuf (>= 3.25, < 5.0)
googleapis-common-protos-types (~> 1.0)
grpc (1.67.0-arm64-darwin)
grpc (1.70.1-arm64-darwin)
google-protobuf (>= 3.25, < 5.0)
googleapis-common-protos-types (~> 1.0)
grpc (1.67.0-x86_64-linux)
grpc (1.70.1-x86_64-linux)
google-protobuf (>= 3.25, < 5.0)
googleapis-common-protos-types (~> 1.0)
haml (5.2.2)
temple (>= 0.8.0)
tilt
hashdiff (1.1.2)
http-accept (1.7.0)
http-cookie (1.0.7)
http-cookie (1.0.8)
domain_name (~> 0.5)
i18n (1.14.6)
i18n (1.14.7)
concurrent-ruby (~> 1.0)
json (2.8.2)
json (2.10.1)
json-schema (2.8.1)
addressable (>= 2.4)
json_pure (2.8.1)
jwt (2.9.3)
jwt (2.10.1)
base64
kgio (2.11.4)
language_server-protocol (3.17.0.3)
language_server-protocol (3.17.0.4)
libxml-ruby (5.0.3)
logger (1.6.1)
lint_roller (1.1.0)
logger (1.6.6)
macaddr (1.7.2)
systemu (~> 2.6.5)
mail (2.8.1)
Expand All @@ -233,35 +237,38 @@ GEM
mime-types (3.6.0)
logger
mime-types-data (~> 3.2015)
mime-types-data (3.2024.1105)
mime-types-data (3.2025.0204)
mini_mime (1.1.5)
minitest (5.25.2)
minitest (5.25.4)
minitest-hooks (1.5.2)
minitest (> 5.3)
minitest-stub_any_instance (1.0.3)
mlanett-redis-lock (0.2.7)
redis
multi_json (1.15.0)
net-http (0.5.0)
net-ftp (0.3.8)
net-protocol
time
net-http (0.6.0)
uri
net-http-persistent (2.9.4)
net-imap (0.4.18)
net-imap (0.5.6)
date
net-protocol
net-pop (0.1.2)
net-protocol
net-protocol (0.2.2)
timeout
net-scp (4.0.0)
net-scp (4.1.0)
net-ssh (>= 2.6.5, < 8.0.0)
net-sftp (4.0.0)
net-ssh (>= 5.0.0, < 8.0.0)
net-smtp (0.5.0)
net-smtp (0.5.1)
net-protocol
net-ssh (7.3.0)
netrc (0.11.0)
newrelic_rpm (9.16.0)
oj (3.16.7)
newrelic_rpm (9.17.0)
oj (3.16.9)
bigdecimal (>= 3.0)
ostruct (>= 0.2)
omni_logger (0.1.4)
Expand All @@ -270,12 +277,12 @@ GEM
ostruct (0.6.1)
parallel (1.26.3)
parseconfig (1.1.2)
parser (3.3.6.0)
parser (3.3.7.1)
ast (~> 2.4.1)
racc
pony (1.13.1)
mail (>= 2.0)
pry (0.15.0)
pry (0.15.2)
coderay (~> 1.1)
method_source (~> 1.0)
public_suffix (6.0.1)
Expand All @@ -293,7 +300,7 @@ GEM
rack (>= 1.2.0)
rack-protection (1.5.5)
rack
rack-test (2.1.0)
rack-test (2.2.0)
rack (>= 1.3)
rack-timeout (0.7.0)
rainbow (3.1.1)
Expand All @@ -304,40 +311,41 @@ GEM
redcarpet (3.6.0)
redis (5.3.0)
redis-client (>= 0.22.0)
redis-client (0.22.2)
redis-client (0.23.2)
connection_pool
redis-rack-cache (2.2.1)
rack-cache (>= 1.10, < 2)
redis-store (>= 1.6, < 2)
redis-store (1.11.0)
redis (>= 4, < 6)
regexp_parser (2.9.2)
regexp_parser (2.10.0)
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)
rexml (3.3.9)
rexml (3.4.1)
rsolr (2.6.0)
builder (>= 2.1.2)
faraday (>= 0.9, < 3, != 2.0.0)
rubocop (1.69.0)
rubocop (1.72.2)
json (~> 2.3)
language_server-protocol (>= 3.17.0)
language_server-protocol (~> 3.17.0.2)
lint_roller (~> 1.1.0)
parallel (~> 1.10)
parser (>= 3.3.0.2)
rainbow (>= 2.2.2, < 4.0)
regexp_parser (>= 2.4, < 3.0)
rubocop-ast (>= 1.36.1, < 2.0)
regexp_parser (>= 2.9.3, < 3.0)
rubocop-ast (>= 1.38.0, < 2.0)
ruby-progressbar (~> 1.7)
unicode-display_width (>= 2.4.0, < 4.0)
rubocop-ast (1.36.1)
rubocop-ast (1.38.0)
parser (>= 3.3.1.0)
ruby-progressbar (1.13.0)
ruby-xxHash (0.4.0.2)
rubyzip (2.3.2)
rubyzip (2.4.1)
rufus-scheduler (2.0.24)
tzinfo (>= 0.3.22)
signet (0.19.0)
Expand Down Expand Up @@ -367,20 +375,23 @@ GEM
rack-test
sinatra (~> 1.4.0)
tilt (>= 1.3, < 3)
sshkit (1.23.2)
sshkit (1.24.0)
base64
logger
net-scp (>= 1.1.2)
net-sftp (>= 2.1.2)
net-ssh (>= 2.8.0)
ostruct
systemu (2.6.5)
temple (0.10.3)
thread_safe (0.3.6)
tilt (2.4.0)
timeout (0.4.2)
tilt (2.6.0)
time (0.4.1)
date
timeout (0.4.3)
tzinfo (1.2.11)
thread_safe (~> 0.1)
unicode-display_width (3.1.2)
unicode-display_width (3.1.4)
unicode-emoji (~> 4.0, >= 4.0.4)
unicode-emoji (4.0.4)
unicorn (6.1.0)
Expand All @@ -396,11 +407,12 @@ GEM
addressable (>= 2.8.0)
crack (>= 0.3.2)
hashdiff (>= 0.4.0, < 2.0.0)
webrick (1.9.0)
webrick (1.9.1)

PLATFORMS
aarch64-linux
arm64-darwin-22
arm64-darwin-24
x86_64-linux

DEPENDENCIES
Expand All @@ -425,6 +437,7 @@ DEPENDENCIES
ncbo_annotator!
ncbo_cron!
ncbo_ontology_recommender!
net-ftp
newrelic_rpm
oj
ontologies_linked_data!
Expand Down Expand Up @@ -458,4 +471,4 @@ DEPENDENCIES
webrick

BUNDLED WITH
2.5.7
2.6.3
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