adding class instances pagination

ontoportal-lirmm · Dec 1, 2021 · 13e2a85 · 13e2a85
1 parent dec0949
commit 13e2a85
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Showing 9 changed files with 116 additions and 68 deletions.
diff --git a/.gitignore b/.gitignore
@@ -31,7 +31,7 @@ bin/**
 
 # Support local configs
 config/environments/*
-!config/environments/config.rb
+!config/environments/development.rb.sample
 !config/environments/config.rb.sample
 
 #ignore capistrano deployment
@@ -54,7 +54,7 @@ test/data/ontology_files/repo/**/*
 
 config/environments/console.rb
 
-config/environments/stage.rb
+config/environments/development.rb.sample
 
 config/environments/benchmark.rb
 

diff --git a/Gemfile b/Gemfile
@@ -46,8 +46,8 @@ gem 'goo', git: 'https://github.com/ontoportal-lirmm/goo.git', branch: 'master'
 gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'master'
 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 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'master'
 gem 'sparql-client', git: 'https://github.com/ncbo/sparql-client.git', branch: 'master'
+gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'master'
 
 # NCBO gems (unversioned)
 gem 'ncbo_resolver', git: 'https://github.com/ncbo/ncbo_resolver.git'

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: ee76178f54dc1a42b4a50028c37fb5c3d86e50da
+  revision: f2e4e8c7430e8c04465f6994db02dcc6f53dcf77
   branch: master
   specs:
     ncbo_ontology_recommender (0.0.1)
@@ -32,7 +32,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: 87bc0e8976519cdcdef06169556677467a10fcfc
+  revision: fb4a89b420f8eb6dda5190a126b6c62e32c4c0c9
   branch: master
   specs:
     sparql-client (1.0.1)
@@ -85,7 +85,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: dea417e105be60619ce4c5f5b4bb4f4ae1d48447
+  revision: d920eedcc78001a28dc96eb4d640c7d0d05f5001
   branch: master
   specs:
     ontologies_linked_data (0.0.1)
@@ -129,29 +129,28 @@ GEM
     addressable (2.3.5)
     airbrussh (1.4.0)
       sshkit (>= 1.6.1, != 1.7.0)
-    backports (3.18.2)
+    backports (3.21.0)
     bcrypt (3.1.16)
     bigdecimal (1.4.2)
     builder (3.2.4)
-    capistrano (3.14.1)
+    capistrano (3.16.0)
       airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
       sshkit (>= 1.9.0)
     capistrano-bundler (2.0.1)
       capistrano (~> 3.1)
-    capistrano-locally (0.2.6)
+    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 (1.1.7)
+    concurrent-ruby (1.1.9)
     cube-ruby (0.0.3)
     dante (0.2.0)
     declarative (0.0.20)
-    declarative-option (0.1.0)
-    docile (1.3.2)
+    docile (1.4.0)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
     elasticsearch (2.0.0)
@@ -162,12 +161,28 @@ GEM
     elasticsearch-transport (2.0.0)
       faraday
       multi_json
-    ethon (0.12.0)
-      ffi (>= 1.3.0)
-    faraday (1.1.0)
+    ethon (0.15.0)
+      ffi (>= 1.15.0)
+    faraday (1.8.0)
+      faraday-em_http (~> 1.0)
+      faraday-em_synchrony (~> 1.0)
+      faraday-excon (~> 1.1)
+      faraday-httpclient (~> 1.0.1)
+      faraday-net_http (~> 1.0)
+      faraday-net_http_persistent (~> 1.1)
+      faraday-patron (~> 1.0)
+      faraday-rack (~> 1.0)
       multipart-post (>= 1.2, < 3)
-      ruby2_keywords
-    ffi (1.13.1)
+      ruby2_keywords (>= 0.0.4)
+    faraday-em_http (1.0.0)
+    faraday-em_synchrony (1.0.0)
+    faraday-excon (1.1.0)
+    faraday-httpclient (1.0.1)
+    faraday-net_http (1.0.1)
+    faraday-net_http_persistent (1.2.0)
+    faraday-patron (1.0.0)
+    faraday-rack (1.0.0)
+    ffi (1.15.4)
     get_process_mem (0.2.7)
       ffi (~> 1.0)
     google-api-client (0.10.3)
@@ -179,41 +194,41 @@ GEM
       mime-types (>= 1.6)
       representable (~> 3.0)
       retriable (>= 2.0, < 4.0)
-    googleauth (0.14.0)
+    googleauth (0.17.1)
       faraday (>= 0.17.3, < 2.0)
       jwt (>= 1.4, < 3.0)
       memoist (~> 0.16)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
-      signet (~> 0.14)
-    haml (5.2.0)
+      signet (~> 0.15)
+    haml (5.2.2)
       temple (>= 0.8.0)
       tilt
     http-accept (1.7.0)
-    http-cookie (1.0.3)
+    http-cookie (1.0.4)
       domain_name (~> 0.5)
     httpclient (2.8.3)
     hurley (0.2)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.3.1)
+    json (2.6.1)
     json-schema (2.5.0)
       addressable (~> 2.3)
-    json_pure (2.3.1)
-    jwt (2.2.2)
-    kgio (2.11.3)
+    json_pure (2.6.1)
+    jwt (2.3.0)
+    kgio (2.11.4)
     libxml-ruby (3.2.1)
-    logger (1.4.2)
+    logger (1.4.4)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.7.1)
       mini_mime (>= 0.1.1)
     memoist (0.16.2)
     method_source (1.0.0)
-    mime-types (3.3.1)
+    mime-types (3.4.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2020.1104)
-    mini_mime (1.0.2)
+    mime-types-data (3.2021.1115)
+    mini_mime (1.1.2)
     minitest (4.7.5)
     minitest-stub_any_instance (1.0.2)
     mlanett-redis-lock (0.2.7)
@@ -226,27 +241,27 @@ GEM
       net-ssh (>= 2.6.5, < 7.0.0)
     net-ssh (6.1.0)
     netrc (0.11.0)
-    newrelic_rpm (6.13.1)
+    newrelic_rpm (8.1.0)
     oj (2.18.5)
     omni_logger (0.1.4)
       logger
-    os (1.1.1)
-    parseconfig (1.0.8)
+    os (1.1.4)
+    parseconfig (1.1.2)
     pony (1.13.1)
       mail (>= 2.0)
-    pry (0.13.1)
+    pry (0.14.1)
       coderay (~> 1.1)
       method_source (~> 1.0)
     rack (1.6.13)
     rack-accept (0.4.5)
       rack (>= 0.4)
     rack-attack (5.4.2)
       rack (>= 1.0, < 3)
-    rack-cache (1.12.1)
+    rack-cache (1.13.0)
       rack (>= 0.4)
     rack-cors (1.0.6)
       rack (>= 1.6.0)
-    rack-mini-profiler (2.2.0)
+    rack-mini-profiler (2.3.3)
       rack (>= 1.2.0)
     rack-protection (1.5.5)
       rack
@@ -257,13 +272,13 @@ GEM
       kgio (~> 2.5)
       rack (>= 1.1, < 3.0)
       unicorn (~> 5.1)
-    raindrops (0.19.1)
+    raindrops (0.19.2)
     rake (10.5.0)
     rdf (1.0.8)
       addressable (>= 2.2)
     recursive-open-struct (1.1.3)
-    redcarpet (3.5.0)
-    redis (4.2.3)
+    redcarpet (3.5.1)
+    redis (4.5.1)
     redis-activesupport (4.1.5)
       activesupport (>= 3, < 5)
       redis-store (~> 1.1.0)
@@ -273,9 +288,9 @@ GEM
     redis-store (1.1.7)
       redis (>= 2.2)
     ref (2.0.0)
-    representable (3.0.4)
+    representable (3.1.1)
       declarative (< 0.1.0)
-      declarative-option (< 0.2.0)
+      trailblazer-option (>= 0.1.1, < 0.2.0)
       uber (< 0.2.0)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
@@ -287,20 +302,22 @@ GEM
       builder (>= 2.1.2)
       faraday (>= 0.9.0)
     ruby-xxHash (0.4.0.1)
-    ruby2_keywords (0.0.2)
-    rubyzip (2.3.0)
+    ruby2_keywords (0.0.5)
+    rubyzip (2.3.2)
     rufus-scheduler (2.0.24)
       tzinfo (>= 0.3.22)
-    sequel (5.38.0)
-    signet (0.14.0)
+    sequel (5.50.0)
+    signet (0.15.0)
       addressable (~> 2.3)
       faraday (>= 0.17.3, < 2.0)
       jwt (>= 1.5, < 3.0)
       multi_json (~> 1.10)
-    simplecov (0.19.1)
+    simplecov (0.21.2)
       docile (~> 1.1)
       simplecov-html (~> 0.11)
+      simplecov_json_formatter (~> 0.1)
     simplecov-html (0.12.3)
+    simplecov_json_formatter (0.1.3)
     sinatra (1.4.8)
       rack (~> 1.5)
       rack-protection (~> 1.4)
@@ -314,26 +331,27 @@ GEM
       rack-test
       sinatra (~> 1.4.0)
       tilt (>= 1.3, < 3)
-    sshkit (1.21.0)
+    sshkit (1.21.2)
       net-scp (>= 1.1.2)
       net-ssh (>= 2.8.0)
     systemu (2.6.5)
     temple (0.8.2)
     tilt (2.0.10)
+    trailblazer-option (0.1.2)
     typhoeus (1.4.0)
       ethon (>= 0.9.0)
-    tzinfo (2.0.3)
+    tzinfo (2.0.4)
       concurrent-ruby (~> 1.0)
     uber (0.1.0)
     unf (0.1.4)
       unf_ext
-    unf_ext (0.0.7.7)
-    unicorn (5.7.0)
+    unf_ext (0.0.8)
+    unicorn (5.8.0)
       kgio (~> 2.6)
       raindrops (~> 0.7)
-    unicorn-worker-killer (0.4.4)
+    unicorn-worker-killer (0.4.5)
       get_process_mem (~> 0)
-      unicorn (>= 4, < 6)
+      unicorn (>= 4, < 7)
     uuid (2.3.9)
       macaddr (~> 1.0)
 

diff --git a/add_ontology_type.rb b/add_ontology_type.rb
@@ -5,7 +5,7 @@
 require_relative 'config/config'
 # require_relative 'config/environments/production'
 # require_relative 'config/environments/stage'
-require_relative 'config/environments/development'
+require_relative 'config/environments/development.rb.sample'
 
 
 value_set_collections = ["NLMVS", "CEDARVS"]

diff --git a/config/unicorn.rb b/config/unicorn.rb
@@ -1,30 +1,30 @@
 application  = 'ontologies_api'
-app_path = "/srv/ncbo/#{application}"
+app_path = "/srv/ontoportal/#{application}"
 working_directory "#{app_path}/current/"
 
 worker_processes 8
-timeout 180 
+timeout 300
 preload_app true
-user "ncbobp", "ncbobp"
+user 'ontoportal', 'ontoportal'
 
-stderr_path "log/unicorn.stderr.log"
-#stdout_path "log/unicorn.stdout.log"
-pid "/var/run/unicorn/unicorn.pid"
+stderr_path 'log/unicorn.stderr.log'
+stdout_path 'log/unicorn.stdout.log'
+pid 'tmp/pids/unicorn.pid'
 
 # Listen on both fast-failing unix data socket (for nginx) & a backloggable TCP connection
-listen "/tmp/unicorn.sock", :backlog => 1024
-listen 8088, :backlog => 256
+listen app_path + '/shared/tmp/sockets/unicorn.sock', :backlog => 1024
+#listen 8087, :backlog => 256
 
 # Make sure unicorn is using current gems after rolling restarts
 before_exec do |server|
-   ENV['BUNDLE_GEMFILE'] = "#{app_path}/current/Gemfile"
+  ENV['BUNDLE_GEMFILE'] = "#{app_path}/current/Gemfile"
 end
 
 before_fork do |server, worker|
   # the following is highly recomended for Rails + "preload_app true"
   # as there's no need for the master process to hold a connection
   defined?(ActiveRecord::Base) and ActiveRecord::Base.connection.disconnect!
- 
+
   ##
   # When sent a USR2, Unicorn will suffix its pidfile with .oldbin and
   # immediately start loading up a new version of itself (loaded with a new
@@ -35,9 +35,9 @@
   # we send it a QUIT.
   #
   # Using this method we get 0 downtime deploys.
- 
+
   old_pid = "#{server.config[:pid]}.oldbin"
- 
+
   if File.exists?(old_pid) && server.pid != old_pid
     begin
       sig = (worker.nr + 1) >= server.worker_processes ? :QUIT : :TTOU
@@ -47,12 +47,12 @@
     end
   end
 end
- 
+
 after_fork do |server, worker|
   # Unicorn master loads the app then forks off workers - because of the way
   # Unix forking works, we need to make sure we aren't using any of the parent's
   # sockets, e.g. db connection
- 
+
   defined?(ActiveRecord::Base) and ActiveRecord::Base.establish_connection
   # Redis and Memcached would go here but their connections are established
   # on demand, so the master never opens a socket

diff --git a/controllers/instances_controller.rb b/controllers/instances_controller.rb
@@ -6,7 +6,8 @@ class InstancesController < ApplicationController
     check_last_modified_segment(LinkedData::Models::Class, [ont.acronym])
     cls = get_class(sub)
     error 404 if cls.nil?
-    reply LinkedData::InstanceLoader.get_instances_by_class(sub.id, cls.id)
+    page, size = page_params
+    reply LinkedData::InstanceLoader.get_instances_by_class(sub.id, cls.id, page, size)
   end
 
   namespace "/ontologies/:ontology/instances" do

diff --git a/lib/rack/slice_detection.rb b/lib/rack/slice_detection.rb
@@ -7,6 +7,7 @@ def initialize(app = nil, options = {})
 
     def call(env)
       if env['HTTP_HOST']
+
         # remove the port if there is one
         domain = env['HTTP_HOST'].gsub(/:\d+$/, '')