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@alexskr
alexskr committed Aug 11, 2022
2 parents bd71d0e + 51ac4c5 commit 3728fab
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9 changes: 2 additions & 7 deletions Gemfile
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@ gem 'activesupport', '~> 3.0'
# see https://github.com/ncbo/ontologies_api/issues/69
gem 'bigdecimal', '1.4.2'
gem 'faraday', '~> 1.9'
gem 'google-api-client', '~> 0.10'
gem 'json-schema', '~> 2.0'
gem 'multi_json', '~> 1.0'
gem 'oj', '~> 2.0'
Expand All @@ -18,13 +17,13 @@ gem 'sinatra-contrib', '~> 1.0'
# Rack middleware
gem 'ffi'
gem 'rack-accept', '~> 0.4'
gem 'rack-attack', '~> 5.4.2', require: 'rack/attack'
gem 'rack-attack', '~> 6.6.1', require: 'rack/attack'
gem 'rack-cache', '~> 1.0'
gem 'rack-cors', require: 'rack/cors'
# GitHub dependency can be removed when https://github.com/niko/rack-post-body-to-params/pull/6 is merged and released
gem 'rack-post-body-to-params', github: 'palexander/rack-post-body-to-params', branch: 'multipart_support'
gem 'rack-timeout'
gem 'redis-rack-cache', '~> 1.0'
gem 'redis-rack-cache', '~> 2.0'

# Data access (caching)
gem 'redis'
Expand All @@ -35,7 +34,6 @@ gem 'cube-ruby', require: 'cube'
gem 'newrelic_rpm'

# HTTP server
gem 'rainbows'
gem 'unicorn'
gem 'unicorn-worker-killer'

Expand All @@ -51,9 +49,6 @@ gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branc
gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'

# NCBO (unversioned)
gem 'ncbo_resolver', github: 'ncbo/ncbo_resolver'

group :development do
gem 'capistrano', '~> 3', require: false
gem 'capistrano-bundler', require: false
Expand Down
84 changes: 28 additions & 56 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/ncbo/goo.git
revision: fd7d45cb862c5c2c1833b64a5c8c14154384edc2
revision: 562826ba21f7da641159071531375776a1414207
branch: master
specs:
goo (0.0.2)
Expand All @@ -15,7 +15,7 @@ GIT

GIT
remote: https://github.com/ncbo/ncbo_annotator.git
revision: ed325ae9f79e3b0a0061b1af0b02f624de1d0eef
revision: 71d41e3afb35dafe29abfb6d9becaadc725bad36
branch: master
specs:
ncbo_annotator (0.0.1)
Expand All @@ -26,7 +26,7 @@ GIT

GIT
remote: https://github.com/ncbo/ncbo_cron.git
revision: 77f7f9ac1596d3a55558d62697c47b73991ee3e8
revision: 5683c127113cf8eee68445413443ba3e164fbed7
branch: master
specs:
ncbo_cron (0.0.1)
Expand All @@ -42,7 +42,7 @@ GIT

GIT
remote: https://github.com/ncbo/ncbo_ontology_recommender.git
revision: b00599b40920cd30e5725862bba5b2609812fb58
revision: 6010ff60b99dc1282822b8a1fb59bd59f453755f
branch: master
specs:
ncbo_ontology_recommender (0.0.1)
Expand All @@ -51,14 +51,6 @@ GIT
ontologies_linked_data
redis

GIT
remote: https://github.com/ncbo/ncbo_resolver.git
revision: 67989c445e53e019b3b3fa4905e0aa9d519df0ed
specs:
ncbo_resolver (0.0.1)
recursive-open-struct
redis

GIT
remote: https://github.com/ncbo/ontologies_linked_data.git
revision: 8196bf34b45c75f8104bb76dfcba1db0f2c048e4
Expand Down Expand Up @@ -113,13 +105,13 @@ GEM
multi_json (~> 1.0)
addressable (2.8.0)
public_suffix (>= 2.0.2, < 5.0)
airbrussh (1.4.0)
airbrussh (1.4.1)
sshkit (>= 1.6.1, != 1.7.0)
backports (3.23.0)
bcrypt (3.1.18)
bigdecimal (1.4.2)
builder (3.2.4)
capistrano (3.17.0)
capistrano (3.17.1)
airbrussh (>= 1.0.0)
i18n
rake (>= 10.0.0)
Expand All @@ -139,7 +131,7 @@ GEM
docile (1.4.0)
domain_name (0.5.20190701)
unf (>= 0.0.5, < 1.0.0)
faraday (1.10.0)
faraday (1.10.1)
faraday-em_http (~> 1.0)
faraday-em_synchrony (~> 1.0)
faraday-excon (~> 1.1)
Expand All @@ -165,15 +157,6 @@ GEM
ffi (1.15.5)
get_process_mem (0.2.7)
ffi (~> 1.0)
google-api-client (0.52.0)
addressable (~> 2.5, >= 2.5.1)
googleauth (~> 0.9)
httpclient (>= 2.8.1, < 3.0)
mini_mime (~> 1.0)
representable (~> 3.0)
retriable (>= 2.0, < 4.0)
rexml
signet (~> 0.12)
google-apis-analytics_v3 (0.10.0)
google-apis-core (>= 0.7, < 2.a)
google-apis-core (0.7.0)
Expand All @@ -185,13 +168,13 @@ GEM
retriable (>= 2.0, < 4.a)
rexml
webrick
googleauth (0.17.1)
faraday (>= 0.17.3, < 2.0)
googleauth (1.2.0)
faraday (>= 0.17.3, < 3.a)
jwt (>= 1.4, < 3.0)
memoist (~> 0.16)
multi_json (~> 1.11)
os (>= 0.9, < 2.0)
signet (~> 0.15)
signet (>= 0.16, < 2.a)
haml (5.2.2)
temple (>= 0.8.0)
tilt
Expand Down Expand Up @@ -226,9 +209,9 @@ GEM
multi_json (1.15.0)
multipart-post (2.2.3)
net-http-persistent (2.9.4)
net-scp (3.0.0)
net-ssh (>= 2.6.5, < 7.0.0)
net-ssh (6.1.0)
net-scp (1.2.1)
net-ssh (>= 2.6.5)
net-ssh (7.0.1)
netrc (0.11.0)
newrelic_rpm (8.9.0)
oj (2.18.5)
Expand All @@ -245,7 +228,7 @@ GEM
rack (1.6.13)
rack-accept (0.4.5)
rack (>= 0.4)
rack-attack (5.4.2)
rack-attack (6.6.1)
rack (>= 1.0, < 3)
rack-cache (1.13.0)
rack (>= 0.4)
Expand All @@ -258,25 +241,20 @@ GEM
rack-test (2.0.2)
rack (>= 1.3)
rack-timeout (0.6.3)
rainbows (5.2.1)
kgio (~> 2.5)
rack (>= 1.1, < 3.0)
unicorn (~> 5.1)
raindrops (0.20.0)
rake (10.5.0)
rdf (1.0.8)
addressable (>= 2.2)
recursive-open-struct (1.1.3)
redcarpet (3.5.1)
redis (4.7.1)
redis-activesupport (4.1.5)
activesupport (>= 3, < 5)
redis-store (~> 1.1.0)
redis-rack-cache (1.2.4)
rack-cache (~> 1.2)
redis-store (~> 1.1.0)
redis-store (1.1.7)
redis (>= 2.2)
redis-activesupport (5.3.0)
activesupport (>= 3, < 8)
redis-store (>= 1.3, < 2)
redis-rack-cache (2.2.1)
rack-cache (>= 1.10, < 2)
redis-store (>= 1.6, < 2)
redis-store (1.9.1)
redis (>= 4, < 5)
representable (3.2.0)
declarative (< 0.1.0)
trailblazer-option (>= 0.1.1, < 0.2.0)
Expand Down Expand Up @@ -328,15 +306,15 @@ GEM
net-ssh (>= 2.8.0)
systemu (2.6.5)
temple (0.8.2)
tilt (2.0.10)
tilt (2.0.11)
trailblazer-option (0.1.2)
tzinfo (2.0.4)
tzinfo (2.0.5)
concurrent-ruby (~> 1.0)
uber (0.1.0)
unf (0.1.4)
unf_ext
unf_ext (0.0.8.2)
unicorn (5.8.0)
unicorn (6.1.0)
kgio (~> 2.6)
raindrops (~> 0.7)
unicorn-worker-killer (0.4.5)
Expand All @@ -347,9 +325,6 @@ GEM
webrick (1.7.0)

PLATFORMS
ruby
x86_64-darwin-19
x86_64-darwin-21
x86_64-linux

DEPENDENCIES
Expand All @@ -363,7 +338,6 @@ DEPENDENCIES
faraday (~> 1.9)
ffi
goo!
google-api-client (~> 0.10)
haml
json-schema (~> 2.0)
minitest (~> 4.0)
Expand All @@ -372,27 +346,25 @@ DEPENDENCIES
ncbo_annotator!
ncbo_cron!
ncbo_ontology_recommender!
ncbo_resolver!
newrelic_rpm
oj (~> 2.0)
ontologies_linked_data!
parseconfig
pry
rack
rack-accept (~> 0.4)
rack-attack (~> 5.4.2)
rack-attack (~> 6.6.1)
rack-cache (~> 1.0)
rack-cors
rack-mini-profiler
rack-post-body-to-params!
rack-test
rack-timeout
rainbows
rake (~> 10.0)
redcarpet
redis
redis-activesupport
redis-rack-cache (~> 1.0)
redis-rack-cache (~> 2.0)
shotgun!
simplecov
simplecov-cobertura
Expand All @@ -404,4 +376,4 @@ DEPENDENCIES
unicorn-worker-killer

BUNDLED WITH
2.3.14
2.3.20
34 changes: 1 addition & 33 deletions Rakefile
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Expand Up @@ -70,38 +70,6 @@ namespace :unicorn do
end
end

namespace :rainbows do
namespace :start do
desc "rainbows start (production settings)"
task :production do
print "Starting rainbows...\n"
`bundle exec rainbows -p 80 -c config/rainbows.rb -D -E production`
end

desc "rainbows start (development settings)"
task :development do
print "Starting rainbows...\n"
`bundle exec rainbows -p 9393 -c config/rainbows.rb`
end
end

desc "rainbows stop"
task :stop do
`pkill -QUIT -f 'rainbows master'`
if $?.exitstatus == 1
puts "rainbows not running"
elsif $?.exitstatus == 0
print "Killing rainbows..."
pids = `pgrep -f 'rainbows master'`
while !pids.empty?
print "."
pids = `pgrep -f 'rainbows master'`
end
print "\n"
end
end
end

def clear_cache(env)
require 'ontologies_linked_data'
require 'ncbo_annotator'
Expand Down Expand Up @@ -142,7 +110,7 @@ namespace :deploy do
`git pull`
puts "Installing bundle"
`bundle install`
puts 'Restarting rainbows'
puts 'Restarting unicorn'
`sudo env PATH=$PATH rake unicorn:stop`
`sudo env PATH=$PATH rake unicorn:start:production`
end
Expand Down
2 changes: 0 additions & 2 deletions config/environments/config.rb.sample
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Expand Up @@ -34,7 +34,5 @@ Annotator.config do |config|
end

LinkedData::OntologiesAPI.config do |config|
config.resolver_redis_host = "localhost"
config.resolver_redis_port = 6379
config.restrict_download = ["ACR0", "ACR1", "ACR2"]
end
3 changes: 0 additions & 3 deletions config/rainbows.rb
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