Feature: Update docker compose to add ncbo cron (#80)

* update config.rb sample with the new SOLR configuration values

* add ncbo_cron service to the API docker compose file and sync the volumes beetween the two

Dockerfile

@@ -23,6 +23,7 @@ RUN bundle install
 
 COPY . /srv/ontoportal/ontologies_api
 RUN cp /srv/ontoportal/ontologies_api/config/environments/config.rb.sample /srv/ontoportal/ontologies_api/config/environments/development.rb
+RUN cp /srv/ontoportal/ontologies_api/config/environments/config.rb.sample /srv/ontoportal/ontologies_api/config/environments/production.rb
 
 EXPOSE 9393
 CMD ["bundle", "exec", "rackup", "-p", "9393", "--host", "0.0.0.0"]

config/environments/config.rb.sample

@@ -19,8 +19,8 @@ REDIS_PORT            = ENV.include?("REDIS_PORT")            ? ENV["REDIS_PORT"
 REPORT_PATH           = ENV.include?("REPORT_PATH")           ? ENV["REPORT_PATH"]           : "./test/ontologies_report.json"
 REPOSITORY_FOLDER     = ENV.include?("REPOSITORY_FOLDER")     ? ENV["REPOSITORY_FOLDER"]     : "./test/data/ontology_files/repo"
 REST_URL_PREFIX       = ENV.include?("REST_URL_PREFIX")       ? ENV["REST_URL_PREFIX"]       : ENV["API_URL"] || "http://localhost:9393"
-SOLR_PROP_SEARCH_URL  = ENV.include?("SOLR_PROP_SEARCH_URL")  ? ENV["SOLR_PROP_SEARCH_URL"]  : "http://localhost:8983/solr/prop_search_core1"
-SOLR_TERM_SEARCH_URL  = ENV.include?("SOLR_TERM_SEARCH_URL")  ? ENV["SOLR_TERM_SEARCH_URL"]  : "http://localhost:8983/solr/term_search_core1"
+SOLR_PROP_SEARCH_URL  = ENV.include?("SOLR_PROP_SEARCH_URL")  ? ENV["SOLR_PROP_SEARCH_URL"]  : "http://localhost:8983/solr"
+SOLR_TERM_SEARCH_URL  = ENV.include?("SOLR_TERM_SEARCH_URL")  ? ENV["SOLR_TERM_SEARCH_URL"]  : "http://localhost:8983/solr"
 
 begin
   # For prefLabel extract main_lang first, or anything if no main found.

config/unicorn.rb

@@ -1,23 +1,45 @@
 application  = 'ontologies_api'
 app_path = "/srv/ontoportal/#{application}"
-working_directory "#{app_path}/current/"
+current_version_path = "#{app_path}/current"
+pid_file_path = 'tmp/pids/unicorn.pid'
 
+if Dir.exists?(current_version_path)
+  app_socket_path = app_path + '/shared/tmp/sockets/unicorn.sock'
+  app_gemfile_path = "#{current_version_path}/Gemfile"
+  user = 'ontoportal'
+else
+  current_version_path = app_path
+  app_gemfile_path = "#{app_path}/Gemfile"
+  app_socket_path = app_path + '/tmp/sockets/unicorn.sock'
+  user = 'root'
+end
+
+working_directory current_version_path
 worker_processes 8
 timeout 300
 preload_app true
-user 'ontoportal', 'ontoportal'
+user user, user
 
 stderr_path 'log/unicorn.stderr.log'
 stdout_path 'log/unicorn.stdout.log'
-pid 'tmp/pids/unicorn.pid'
 
+
+require 'fileutils'
+[pid_file_path, app_socket_path].each do |file_path|
+  directory_path = File.dirname(file_path)
+  FileUtils.mkdir_p(directory_path) unless Dir.exist?(File.dirname(file_path))
+end
+
+
+
+pid  pid_file_path
 # Listen on both fast-failing unix data socket (for nginx) & a backloggable TCP connection
-listen app_path + '/shared/tmp/sockets/unicorn.sock', :backlog => 1024
+listen app_socket_path, :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_gemfile_path
 end
 
 before_fork do |server, worker|

docker-compose.yml

@@ -1,31 +1,27 @@
 x-app: &app
-  image: agroportal/ontologies_api:development
+  image: agroportal/ontologies_api:master
   environment: &env
     # default bundle config resolves to /usr/local/bundle/config inside of the container
     # we are setting it to local app directory if we need to use 'bundle config local'
-    BUNDLE_APP_CONFIG: /srv/ontoportal/ontologies_api/.bundle
     BUNDLE_PATH: /srv/ontoportal/bundle
     COVERAGE: 'true' # enable simplecov code coverage
     REDIS_HOST: redis-ut
     REDIS_PORT: 6379
     SOLR_TERM_SEARCH_URL: http://solr-ut:8983/solr
     SOLR_PROP_SEARCH_URL: http://solr-ut:8983/solr
+    GOO_BACKEND_NAME: 4store
+    GOO_PORT: 9000
+    GOO_HOST: 4store-ut
+    MGREP_HOST: mgrep-ut
+    MGREP_PORT: 55555
+    REPOSITORY_FOLDER: /srv/ontoportal/data/repository
+    REPORT_PATH: /srv/ontoportal/data/reports/ontologies_report.json
+    MGREP_DICTIONARY_FILE: /srv/ontoportal/data/mgrep
   stdin_open: true
   tty: true
   command: /bin/bash
-  volumes:
-    # bundle volume for hosting gems installed by bundle; it speeds up gem install in local development
-    - bundle:/srv/ontoportal/bundle
-    - .:/srv/ontoportal/ontologies_api
-    # mount directory containing development version of the gems if you need to use 'bundle config local'
-    #- /Users/alexskr/ontoportal:/Users/alexskr/ontoportal
-  depends_on: &depends_on
-    solr-prop-ut:
-      condition: service_healthy
-    solr-term-ut:
-      condition: service_healthy
-    redis-ut:
-      condition: service_healthy
+
+
 
 services:
   api:
@@ -34,21 +30,55 @@ services:
       .env
     environment:
       <<: *env
-      GOO_BACKEND_NAME: 4store
-      GOO_PORT: 9000
-      GOO_HOST: 4store-ut
-      GOO_PATH_QUERY: /sparql/
-      GOO_PATH_DATA: /data/
-      GOO_PATH_UPDATE: /update/
+      BUNDLE_APP_CONFIG: /srv/ontoportal/ontologies_api/.bundle
     profiles:
       - 4store
     depends_on:
-      - solr-ut
-      - redis-ut
-      - mgrep-ut
-      - 4store-ut
+      solr-ut:
+        condition: service_healthy
+      redis-ut:
+        condition: service_healthy
+      mgrep-ut:
+        condition: service_started
+      4store-ut:
+        condition: service_started
+      ncbo_cron:
+        condition: service_started
     ports:
       - "9393:9393"
+    volumes:
+      # bundle volume for hosting gems installed by bundle; it speeds up gem install in local development
+      - app_api:/srv/ontoportal/ontologies_api
+      - repository:/srv/ontoportal/data/repository
+
+  ncbo_cron:
+    <<: *app
+    image: agroportal/ncbo_cron:master
+    env_file:
+      .env
+    environment:
+      <<: *env
+      BUNDLE_APP_CONFIG: /srv/ontoportal/ncbo_cron/.bundle
+    command: "bundle exec bin/ncbo_cron"
+    profiles:
+      - 4store
+    volumes:
+      - app_cron:/srv/ontoportal/ncbo_cron
+      - repository:/srv/ontoportal/data/repository
+      - history:/usr/local/hist
+      - reports:/srv/ontoportal/data/reports
+      - mgrep:/srv/ontoportal/data/mgrep
+      - logs:/srv/ontoportal/ncbo_cron/logs
+    depends_on:
+      solr-ut:
+        condition: service_healthy
+      redis-ut:
+        condition: service_healthy
+      mgrep-ut:
+        condition: service_started
+      4store-ut:
+        condition: service_started
+
 
   mgrep-ut:
     image: ontoportal/mgrep-ncbo:0.1
@@ -84,8 +114,14 @@ services:
     ports:
       - 8983:8983
     command: bin/solr start -cloud -f
-   # volumes:
-      #- solr_data:/var/solr/data
+    volumes:
+      - solr_data:/var/solr/data
+    healthcheck:
+      test: [ "CMD", "curl", "-f", "http://localhost:8983/solr/admin/info/system?wt=json" ]
+      interval: 30s
+      timeout: 10s
+      retries: 3
+
   agraph-ut:
     image: franzinc/agraph:v8.1.0
     platform: linux/amd64
@@ -152,7 +188,13 @@ services:
       - gb
 
 volumes:
-  bundle:
+  app_api:
+  app_cron:
   agdata:
   4store:
-  #solr_data:
+  repository:
+  solr_data:
+  reports:
+  mgrep:
+  logs:
+  history: