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Merge to master: AgroPortal release 2.8.0
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syphax-bouazzouni committed Jul 8, 2024
1 parent 77926d5 commit d9dc5c3
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8 changes: 4 additions & 4 deletions Gemfile
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ gem 'json-ld'


# Rack middleware
gem 'ffi'
gem 'ffi', '~> 1.15.5'
gem 'rack-accept', '~> 0.4'
gem 'rack-attack', '~> 6.6.1', require: 'rack/attack'
gem 'rack-cache', '~> 1.13.0'
Expand Down Expand Up @@ -47,11 +47,11 @@ gem 'redcarpet'

# NCBO gems (can be from a local dev path or from rubygems/git)
gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'development'
gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'master'
gem 'ncbo_ontology_recommender', git: 'https://github.com/ncbo/ncbo_ontology_recommender.git', branch: 'master'
gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'development'
gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'development'
gem 'ontologies_linked_data', git: 'https://github.com/lifewatch-eric/ontologies_linked_data.git', branch: 'master'
gem 'ncbo_cron', git: 'https://github.com/lifewatch-eric/ncbo_cron.git', branch: 'master'

group :development do
# bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42
Expand All @@ -77,4 +77,4 @@ group :test do
gem 'simplecov', require: false
gem 'simplecov-cobertura' # for codecov.io
gem 'webmock', '~> 3.19.1'
end
end
99 changes: 55 additions & 44 deletions Gemfile.lock
Original file line number Diff line number Diff line change
@@ -1,3 +1,40 @@
GIT
remote: https://github.com/lifewatch-eric/ncbo_cron.git
revision: 2ff764e536e049220208e3cd6c0ee9f03366df17
branch: master
specs:
ncbo_cron (0.0.1)
dante
goo
google-analytics-data
google-apis-analytics_v3
mlanett-redis-lock
multi_json
ncbo_annotator
ontologies_linked_data
redis
rufus-scheduler (~> 2.0.24)

GIT
remote: https://github.com/lifewatch-eric/ontologies_linked_data.git
revision: c212a601a796e43c6ede014afe74da78858612a3
branch: master
specs:
ontologies_linked_data (0.0.1)
activesupport
bcrypt
goo
json
libxml-ruby
multi_json
oj
omni_logger
pony
rack
rack-test
rsolr
rubyzip

GIT
remote: https://github.com/ncbo/ncbo_ontology_recommender.git
revision: 013abea4af3b10910ec661dbb358a4b6cae198a4
Expand All @@ -11,7 +48,7 @@ GIT

GIT
remote: https://github.com/ontoportal-lirmm/goo.git
revision: b2a635fb1e8206e6e3010be4dbe033b47eb58481
revision: a95245b8c964431505ca6315907440996c59a00d
branch: development
specs:
goo (0.0.2)
Expand All @@ -38,43 +75,6 @@ GIT
redis
ruby-xxHash

GIT
remote: https://github.com/ontoportal-lirmm/ncbo_cron.git
revision: fabd04ef4fa37989d526fc6a7aa1e98830008dae
branch: master
specs:
ncbo_cron (0.0.1)
dante
goo
google-analytics-data
google-apis-analytics_v3
mlanett-redis-lock
multi_json
ncbo_annotator
ontologies_linked_data
redis
rufus-scheduler (~> 2.0.24)

GIT
remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
revision: a5b56a68e6dc8ecfc9db708d44350342dac38ce6
branch: development
specs:
ontologies_linked_data (0.0.1)
activesupport
bcrypt
goo
json
libxml-ruby
multi_json
oj
omni_logger
pony
rack
rack-test
rsolr
rubyzip

GIT
remote: https://github.com/ontoportal-lirmm/sparql-client.git
revision: 59251e59346c9a69a67c88552ba55a1244eec602
Expand Down Expand Up @@ -114,9 +114,10 @@ GEM
base64 (0.2.0)
bcrypt (3.1.20)
bcrypt_pbkdf (1.1.1)
bcrypt_pbkdf (1.1.1-x86_64-darwin)
bigdecimal (1.4.2)
builder (3.3.0)
capistrano (3.19.0)
capistrano (3.19.1)
airbrussh (>= 1.0.0)
i18n
rake (>= 10.0.0)
Expand Down Expand Up @@ -164,7 +165,7 @@ GEM
faraday-patron (1.0.0)
faraday-rack (1.0.0)
faraday-retry (1.0.3)
ffi (1.17.0-x86_64-linux-gnu)
ffi (1.15.5)
gapic-common (0.21.1)
faraday (>= 1.9, < 3.a)
faraday-retry (>= 1.0, < 3.a)
Expand Down Expand Up @@ -197,6 +198,8 @@ 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 (1.6.0)
google-protobuf (>= 3.18, < 5.a)
Expand All @@ -211,6 +214,12 @@ GEM
multi_json (~> 1.11)
os (>= 0.9, < 2.0)
signet (>= 0.16, < 2.a)
grpc (1.64.0)
google-protobuf (~> 3.25)
googleapis-common-protos-types (~> 1.0)
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)
Expand Down Expand Up @@ -247,7 +256,7 @@ GEM
method_source (1.1.0)
mime-types (3.5.2)
mime-types-data (~> 3.2015)
mime-types-data (3.2024.0604)
mime-types-data (3.2024.0702)
mini_mime (1.1.5)
minitest (4.7.5)
minitest-stub_any_instance (1.0.3)
Expand Down Expand Up @@ -385,7 +394,7 @@ GEM
strscan (3.1.0)
systemu (2.6.5)
temple (0.10.3)
tilt (2.3.0)
tilt (2.4.0)
timeout (0.4.1)
trailblazer-option (0.1.2)
tzinfo (2.0.6)
Expand All @@ -405,6 +414,8 @@ GEM
hashdiff (>= 0.4.0, < 2.0.0)

PLATFORMS
ruby
x86_64-darwin-23
x86_64-linux

DEPENDENCIES
Expand All @@ -418,7 +429,7 @@ DEPENDENCIES
cube-ruby
ed25519 (>= 1.2, < 2.0)
faraday (~> 1.9)
ffi
ffi (~> 1.15.5)
goo!
haml (~> 5.2.2)
json-ld
Expand Down Expand Up @@ -462,4 +473,4 @@ DEPENDENCIES
webmock (~> 3.19.1)

BUNDLED WITH
2.3.23
2.4.22
9 changes: 6 additions & 3 deletions config/deploy.rb
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
APP_PATH = '/srv/ontoportal'

set :application, 'ontologies_api'
set :repo_url, "https://github.com/ncbo/#{fetch(:application)}.git"
set :repo_url, "https://github.com/lifewatch-eric/#{fetch(:application)}.git"

set :deploy_via, :remote_cache

Expand Down Expand Up @@ -31,6 +31,9 @@
# Default value for linked_dirs is []
# set :linked_dirs, %w{log tmp/pids tmp/cache tmp/sockets vendor/bundle public/system}
set :linked_dirs, %w{log vendor/bundle tmp/pids tmp/sockets public/system}
append :linked_files, "config/unicorn.rb"
append :linked_dirs, 'config/environments', 'log', 'tmp', '.bundle'


# rbenv
# set :rbenv_type, :system #or :user
Expand Down Expand Up @@ -105,8 +108,8 @@
end
end

after :publishing, :get_config
after :get_config, :restart
after :publishing, :restart
#after :get_config, :restart
# after :deploy, :smoke_test

after :restart, :clear_cache do
Expand Down
49 changes: 0 additions & 49 deletions config/deploy/appliance.rb

This file was deleted.

48 changes: 11 additions & 37 deletions config/deploy/production.rb
Original file line number Diff line number Diff line change
@@ -1,39 +1,13 @@
# Simple Role Syntax
# ==================
# Supports bulk-adding hosts to roles, the primary
# server in each group is considered to be the first
# unless any hosts have the primary property set.
# Don't declare `role :all`, it's a meta role
role :app, %w{[email protected]}
role :web, %w{[email protected]}
role :db, %w{[email protected]}
set :branch, 'master'
set :server, 'ecoportal.lifewatch.eu'

# Extended Server Syntax
# ======================
# This can be used to drop a more detailed server
# definition into the server list. The second argument
# something that quacks like a hash can be used to set
# extended properties on the server.
server 'example.com', user: 'deploy', roles: %w{web app}, my_property: :my_value
server fetch(:server), user: fetch(:user), roles: %w{web app}

# you can set custom ssh options
# it's possible to pass any option but you need to keep in mind that net/ssh understand limited list of options
# you can see them in [net/ssh documentation](http://net-ssh.github.io/net-ssh/classes/Net/SSH.html#method-c-start)
# set it globally
# set :ssh_options, {
# keys: %w(/home/rlisowski/.ssh/id_rsa),
# forward_agent: false,
# auth_methods: %w(password)
# }
# and/or per server
# server 'example.com',
# user: 'user_name',
# roles: %w{web app},
# ssh_options: {
# user: 'user_name', # overrides user setting above
# keys: %w(/home/user_name/.ssh/id_rsa),
# forward_agent: false,
# auth_methods: %w(publickey password)
# # password: 'please use keys'
# }
# setting per server overrides global ssh_options
set :ssh_options, {
user: 'ontoportal',
forward_agent: 'true',
#keys: %w(config/deploy_id_rsa),
#auth_methods: %w(publickey),
# use ssh proxy if UI servers are on a private network
#proxy: Net::SSH::Proxy::Command.new('ssh [email protected] -W %h:%p')
}
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