Hierarchy view issue

[fillies]

Hi everyone,

we are facing the issue that for certain classes of ontologies, when extended by pressing the plus in the hierarchy view, a long loading time and an error due to empty responses appears. Example: https://biodivportal.gfbio.org/ontologies/ITIS/?p=classes. It seems like the requested resource was not found. I am quite new to the application, our first idea was a lack of compuational resources but it seems not to be the issues. Do you have any inside on this?

Logs /var/log/rails/appliance.log:

/srv/ontoportal/.bundle/ruby/2.7.0/gems/multi_json-1.15.0/lib/multi_json/adapters/oj.rb:34:in `load'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/multi_json-1.15.0/lib/multi_json/adapters/oj.rb:34:in `load'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/multi_json-1.15.0/lib/multi_json/adapter.rb:21:in `load'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/multi_json-1.15.0/lib/multi_json.rb:122:in `load'
        /srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_api_ruby_client-941f4c615e37/lib/ontologies_api_client/http.rb:274:in `load_json'
        /srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_api_ruby_client-941f4c615e37/lib/ontologies_api_client/http.rb:145:in `object_from_json'
        /srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_api_ruby_client-941f4c615e37/lib/ontologies_api_client/middleware/faraday-object-cache.rb:94:in `block in call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/faraday-2.0.1/lib/faraday/response.rb:42:in `on_complete'
        /srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_api_ruby_client-941f4c615e37/lib/ontologies_api_client/middleware/faraday-object-cache.rb:63:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_api_ruby_client-941f4c615e37/lib/ontologies_api_client/middleware/faraday-last-updated.rb:16:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_api_ruby_client-941f4c615e37/lib/ontologies_api_client/middleware/faraday-slices.rb:16:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_api_ruby_client-941f4c615e37/lib/ontologies_api_client/middleware/faraday-user-apikey.rb:16:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/faraday-2.0.1/lib/faraday/rack_builder.rb:153:in `build_response'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/faraday-2.0.1/lib/faraday/connection.rb:445:in `run_request'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/faraday-2.0.1/lib/faraday/connection.rb:200:in `get'
        /srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_api_ruby_client-941f4c615e37/lib/ontologies_api_client/http.rb:63:in `get'
        /srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_api_ruby_client-941f4c615e37/lib/ontologies_api_client/collection.rb:28:in `top_level_links'
        /srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_api_ruby_client-941f4c615e37/lib/ontologies_api_client/collection.rb:43:in `entry_point'
        /srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_api_ruby_client-941f4c615e37/lib/ontologies_api_client/collection.rb:56:in `all'
        /srv/ontoportal/bioportal_web_ui/releases/20220602203400/app/controllers/home_controller.rb:5:in `index'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_controller/metal/basic_implicit_render.rb:6:in `send_action'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/abstract_controller/base.rb:195:in `process_action'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_controller/metal/rendering.rb:30:in `process_action'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/abstract_controller/callbacks.rb:42:in `block in process_action'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/activesupport-6.0.4.1/lib/active_support/callbacks.rb:135:in `run_callbacks'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/abstract_controller/callbacks.rb:41:in `process_action'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_controller/metal/rescue.rb:22:in `process_action'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_controller/metal/instrumentation.rb:33:in `block in process_action'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/activesupport-6.0.4.1/lib/active_support/notifications.rb:180:in `block in instrument'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/activesupport-6.0.4.1/lib/active_support/notifications/instrumenter.rb:24:in `instrument'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/activesupport-6.0.4.1/lib/active_support/notifications.rb:180:in `instrument'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_controller/metal/instrumentation.rb:32:in `process_action'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_controller/metal/params_wrapper.rb:245:in `process_action'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/activerecord-6.0.4.1/lib/active_record/railties/controller_runtime.rb:27:in `process_action'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/abstract_controller/base.rb:136:in `process'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionview-6.0.4.1/lib/action_view/rendering.rb:39:in `process'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_controller/metal.rb:190:in `dispatch'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_controller/metal.rb:254:in `dispatch'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/routing/route_set.rb:50:in `dispatch'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/routing/route_set.rb:33:in `serve'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/journey/router.rb:49:in `block in serve'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/journey/router.rb:32:in `each'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/journey/router.rb:32:in `serve'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/routing/route_set.rb:834:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-2.2.3/lib/rack/tempfile_reaper.rb:15:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-2.2.3/lib/rack/etag.rb:27:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-2.2.3/lib/rack/conditional_get.rb:27:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-2.2.3/lib/rack/head.rb:12:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/http/content_security_policy.rb:18:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-2.2.3/lib/rack/session/abstract/id.rb:266:in `context'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-2.2.3/lib/rack/session/abstract/id.rb:260:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/middleware/cookies.rb:654:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/middleware/callbacks.rb:27:in `block in call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/activesupport-6.0.4.1/lib/active_support/callbacks.rb:101:in `run_callbacks'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/middleware/callbacks.rb:26:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/middleware/actionable_exceptions.rb:18:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/middleware/debug_exceptions.rb:32:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/middleware/show_exceptions.rb:33:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/railties-6.0.4.1/lib/rails/rack/logger.rb:37:in `call_app'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/railties-6.0.4.1/lib/rails/rack/logger.rb:26:in `block in call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/activesupport-6.0.4.1/lib/active_support/tagged_logging.rb:80:in `block in tagged'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/activesupport-6.0.4.1/lib/active_support/tagged_logging.rb:28:in `tagged'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/activesupport-6.0.4.1/lib/active_support/tagged_logging.rb:80:in `tagged'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/railties-6.0.4.1/lib/rails/rack/logger.rb:26:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/middleware/remote_ip.rb:81:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/middleware/request_id.rb:27:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-2.2.3/lib/rack/method_override.rb:24:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-2.2.3/lib/rack/runtime.rb:22:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/activesupport-6.0.4.1/lib/active_support/cache/strategy/local_cache_middleware.rb:29:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/middleware/executor.rb:14:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-2.2.3/lib/rack/sendfile.rb:110:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/actionpack-6.0.4.1/lib/action_dispatch/middleware/host_authorization.rb:76:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-mini-profiler-3.0.0/lib/mini_profiler/profiler.rb:249:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/railties-6.0.4.1/lib/rails/engine.rb:527:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/railties-6.0.4.1/lib/rails/railtie.rb:190:in `public_send'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/railties-6.0.4.1/lib/rails/railtie.rb:190:in `method_missing'
        /usr/share/ruby/vendor_ruby/phusion_passenger/rack/thread_handler_extension.rb:107:in `process_request'
        /usr/share/ruby/vendor_ruby/phusion_passenger/request_handler/thread_handler.rb:149:in `accept_and_process_next_request'
        /usr/share/ruby/vendor_ruby/phusion_passenger/request_handler/thread_handler.rb:110:in `main_loop'
        /usr/share/ruby/vendor_ruby/phusion_passenger/request_handler.rb:419:in `block (3 levels) in start_threads'
        /usr/share/ruby/vendor_ruby/phusion_passenger/utils.rb:113:in `block in create_thread_and_abort_on_exception'):

/srv/ontoportal/ontologies_api/shared/log/unicorn.stderr.log

cache error: unknown keywords: :scheme, :namespace, :raw
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-client-0.14.1/lib/redis_client/config.rb:21:in `initialize'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-client-0.14.1/lib/redis_client/config.rb:184:in `initialize'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-client-0.14.1/lib/redis_client.rb:143:in `new'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-client-0.14.1/lib/redis_client.rb:143:in `config'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-5.0.6/lib/redis/client.rb:23:in `config'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-5.0.6/lib/redis.rb:157:in `initialize_client'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-5.0.6/lib/redis.rb:73:in `initialize'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-store-1.9.2/lib/redis/store.rb:17:in `initialize'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-store-1.9.2/lib/redis/store/factory.rb:26:in `new'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-store-1.9.2/lib/redis/store/factory.rb:26:in `create'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-store-1.9.2/lib/redis/store/factory.rb:9:in `create'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-rack-cache-2.2.1/lib/rack/cache/redis_base.rb:25:in `initialize'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-rack-cache-2.2.1/lib/rack/cache/redis_base.rb:20:in `new'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-rack-cache-2.2.1/lib/rack/cache/redis_base.rb:20:in `resolve'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-cache-1.13.0/lib/rack/cache/storage.rb:39:in `create_store'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-cache-1.13.0/lib/rack/cache/storage.rb:18:in `resolve_metastore_uri'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-cache-1.13.0/lib/rack/cache/context.rb:35:in `metastore'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-cache-1.13.0/lib/rack/cache/context.rb:176:in `lookup'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-cache-1.13.0/lib/rack/cache/context.rb:67:in `call!'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-cache-1.13.0/lib/rack/cache/context.rb:52:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-9b90ad0483b6/lib/ontologies_linked_data/security/access_denied_middleware.rb:10:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_linked_data-9b90ad0483b6/lib/ontologies_linked_data/security/authorization.rb:45:in `call'
/srv/ontoportal/ontologies_api/releases/20230228134244/lib/rack/param_translator.rb:47:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/rack-post-body-to-params-0fd30e710386/lib/rack/post-body-to-params.rb:144:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-accept-0.4.5/lib/rack/accept/context.rb:22:in `call'
/srv/ontoportal/ontologies_api/releases/20230228134244/lib/rack/slice_detection.rb:36:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-cors-1.0.6/lib/rack/cors.rb:98:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-cors-1.0.6/lib/rack/cors.rb:98:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-1.6.13/lib/rack/static.rb:124:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-1.6.13/lib/rack/commonlogger.rb:33:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:219:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-protection-1.5.5/lib/rack/protection/xss_header.rb:18:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-protection-1.5.5/lib/rack/protection/json_csrf.rb:18:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-protection-1.5.5/lib/rack/protection/base.rb:49:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-protection-1.5.5/lib/rack/protection/base.rb:49:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-protection-1.5.5/lib/rack/protection/frame_options.rb:31:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-1.6.13/lib/rack/logger.rb:15:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-1.6.13/lib/rack/commonlogger.rb:33:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:219:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:212:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-1.6.13/lib/rack/head.rb:13:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-1.6.13/lib/rack/methodoverride.rb:22:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:182:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:2013:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1487:in `block in call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1787:in `synchronize'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1487:in `call'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/unicorn-6.1.0/lib/unicorn/http_server.rb:634:in `process_client'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/unicorn-worker-killer-0.4.5/lib/unicorn/worker_killer.rb:53:in `process_client'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/unicorn-worker-killer-0.4.5/lib/unicorn/worker_killer.rb:93:in `process_client'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/unicorn-6.1.0/lib/unicorn/http_server.rb:739:in `worker_loop'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/unicorn-6.1.0/lib/unicorn/http_server.rb:547:in `spawn_missing_workers'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/unicorn-6.1.0/lib/unicorn/http_server.rb:143:in `start'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/unicorn-6.1.0/bin/unicorn:128:in `<top (required)>'
/srv/ontoportal/.bundle/ruby/2.7.0/bin/unicorn:23:in `load'
/srv/ontoportal/.bundle/ruby/2.7.0/bin/unicorn:23:in `<top (required)>'
/home/ontoportal/.gem/ruby/2.7.0/gems/bundler-2.3.26/lib/bundler/cli/exec.rb:58:in `load'
/home/ontoportal/.gem/ruby/2.7.0/gems/bundler-2.3.26/lib/bundler/cli/exec.rb:58:in `kernel_load'
/home/ontoportal/.gem/ruby/2.7.0/gems/bundler-2.3.26/lib/bundler/cli/exec.rb:23:in `run'
/home/ontoportal/.gem/ruby/2.7.0/gems/bundler-2.3.26/lib/bundler/cli.rb:486:in `exec'
/home/ontoportal/.gem/ruby/2.7.0/gems/bundler-2.3.26/lib/bundler/vendor/thor/lib/thor/command.rb:27:in `run'
/home/ontoportal/.gem/ruby/2.7.0/gems/bundler-2.3.26/lib/bundler/vendor/thor/lib/thor/invocation.rb:127:in `invoke_command'
/home/ontoportal/.gem/ruby/2.7.0/gems/bundler-2.3.26/lib/bundler/vendor/thor/lib/thor.rb:392:in `dispatch'
/home/ontoportal/.gem/ruby/2.7.0/gems/bundler-2.3.26/lib/bundler/cli.rb:31:in `dispatch'
/home/ontoportal/.gem/ruby/2.7.0/gems/bundler-2.3.26/lib/bundler/vendor/thor/lib/thor/base.rb:485:in `start'
/home/ontoportal/.gem/ruby/2.7.0/gems/bundler-2.3.26/lib/bundler/cli.rb:25:in `start'
/home/ontoportal/.gem/ruby/2.7.0/gems/bundler-2.3.26/exe/bundle:48:in `block in <top (required)>'
/home/ontoportal/.gem/ruby/2.7.0/gems/bundler-2.3.26/lib/bundler/friendly_errors.rb:120:in `with_friendly_errors'
/home/ontoportal/.gem/ruby/2.7.0/gems/bundler-2.3.26/exe/bundle:36:in `<top (required)>'
/usr/local/rbenv/versions/2.7.6/bin/bundle:23:in `load'
/usr/local/rbenv/versions/2.7.6/bin/bundle:23:in `<main>'

134.176.27.225, 192.168.0.13 - admin [28/Feb/2024:07:49:36 +0000] "GET /ontologies/ITIS/latest_submission?include=all&include_status=ready HTTP/1.0" 200 16512 0.0887
cache error: unknown keywords: :scheme, :namespace, :raw
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-client-0.14.1/lib/redis_client/config.rb:21:in `initialize'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-client-0.14.1/lib/redis_client/config.rb:184:in `initialize'
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/srv/ontoportal/.bundle/ruby/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:212:in `call'
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/home/ontoportal/.gem/ruby/2.7.0/gems/bundler-2.3.26/lib/bundler/cli.rb:486:in `exec'
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/home/ontoportal/.gem/ruby/2.7.0/gems/bundler-2.3.26/exe/bundle:36:in `<top (required)>'
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134.176.27.225, 192.168.0.13 - admin [28/Feb/2024:07:49:36 +0000] "GET /ontologies/ITIS/classes/http%3A%2F%2Fterminologies.gfbio.org%2FITIS%2FTaxa_0?include=prefLabel%2Cdefinition%2Csynonym%2Cobsolete%2Cproperties%2ChasChildren%2Cchildre%2CinScheme%2CmemberOf HTTP/1.0" 200 2820 0.0438
cache error: unknown keywords: :scheme, :namespace, :raw
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-client-0.14.1/lib/redis_client/config.rb:21:in `initialize'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-client-0.14.1/lib/redis_client/config.rb:184:in `initialize'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-client-0.14.1/lib/redis_client.rb:143:in `new'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-client-0.14.1/lib/redis_client.rb:143:in `config'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-5.0.6/lib/redis/client.rb:23:in `config'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-5.0.6/lib/redis.rb:157:in `initialize_client'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-5.0.6/lib/redis.rb:73:in `initialize'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-store-1.9.2/lib/redis/store.rb:17:in `initialize'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-store-1.9.2/lib/redis/store/factory.rb:26:in `new'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-store-1.9.2/lib/redis/store/factory.rb:26:in `create'
/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-store-1.9.2/lib/redis/store/factory.rb:9:in `create'
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/srv/ontoportal/.bundle/ruby/2.7.0/gems/redis-rack-cache-2.2.1/lib/rack/cache/redis_base.rb:20:in `new'
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/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-cache-1.13.0/lib/rack/cache/context.rb:176:in `lookup'
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/srv/ontoportal/.bundle/ruby/2.7.0/gems/rack-1.6.13/lib/rack/static.rb:124:in `call'
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srv/ontoportal/bioportal_web_ui/shared/log/

Faraday::TimeoutError (Problem retrieving:
https://data.biodiv-onto.gfbio.dev/ontologies/ITIS/classes?display=prefLabel%2Cmodified%2Ccreated&include=prefLabel%2Cdefinition%2Csynonym%2Cobsolete%2ChasChildren%2CinScheme%2CmemberOf&order=desc%2Cdesc&page=1&sortby=modified%2Ccreated

Error: read timeout reached
/srv/ontoportal/.bundle/ruby/2.7.0/gems/excon-0.99.0/lib/excon/socket.rb:88:in `rescue in readline'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/excon-0.99.0/lib/excon/socket.rb:83:in `readline'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/excon-0.99.0/lib/excon/response.rb:73:in `block in parse'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/excon-0.99.0/lib/excon/response.rb:72:in `loop'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/excon-0.99.0/lib/excon/response.rb:72:in `parse'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/excon-0.99.0/lib/excon/middlewares/response_parser.rb:7:in `response_call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/excon-0.99.0/lib/excon/connection.rb:459:in `response'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/excon-0.99.0/lib/excon/connection.rb:290:in `request'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/faraday-excon-2.0.0/lib/faraday/adapter/excon.rb:29:in `block in call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/faraday-2.0.1/lib/faraday/adapter.rb:45:in `connection'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/faraday-excon-2.0.0/lib/faraday/adapter/excon.rb:29:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/faraday-2.0.1/lib/faraday/request/url_encoded.rb:25:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/faraday-multipart-1.0.4/lib/faraday/multipart/middleware.rb:28:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_api_ruby_client-7b298ff96e46/lib/ontologies_api_client/middleware/faraday-last-updated.rb:16:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_api_ruby_client-7b298ff96e46/lib/ontologies_api_client/middleware/faraday-slices.rb:16:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/bundler/gems/ontologies_api_ruby_client-7b298ff96e46/lib/ontologies_api_client/middleware/faraday-user-apikey.rb:16:in `call'
        /srv/ontoportal/.bundle/ruby/2.7.0/gems/faraday-2.0.1/lib/faraday/rack_builder.rb:153:in `build_response'
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        /srv/ontoportal/.bundle/ruby/2.7.0/gems/faraday-2.0.1/lib/faraday/connection.rb:200:in `get'
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app/controllers/application_controller.rb:483:in `get_class'
app/controllers/ontologies_controller.rb:152:in `classes'
app/controllers/ontologies_controller.rb:354:in `show'
F, [2024-02-01T09:55:23.128440 #12520] FATAL -- :
ActionController::RoutingError (No route matches [OPTIONS] "/ajax/properties/tree"):

F, [2024-02-01T13:06:06.226667 #29596] FATAL -- :
ActionController::RoutingError (No route matches [GET] "/wp-login.php"):

F, [2024-02-01T13:08:54.693347 #29596] FATAL -- :
ActionController::RoutingError (No route matches [GET] "/wp-login.php"):

F, [2024-02-01T13:08:54.994188 #29596] FATAL -- :
ActionController::RoutingError (No route matches [GET] "/xmlrpc.php"):

F, [2024-02-01T13:08:55.758774 #29596] FATAL -- :
ActionController::RoutingError (No route matches [GET] "/wp-login.php"):

F, [2024-02-01T13:08:56.284795 #29596] FATAL -- :
ActionController::RoutingError (No route matches [GET] "/xmlrpc.php"):

F, [2024-02-01T13:51:25.168443 #10699] FATAL -- :
ActionController::RoutingError (No route matches [OPTIONS] "/ajax/properties/tree"):

F, [2024-02-01T13:52:03.461759 #10849] FATAL -- :
ActionController::RoutingError (No route matches [OPTIONS] "/ajax/properties/tree"):

F, [2024-02-01T17:25:47.212930 #29596] FATAL -- :
NameError (wrong constant name Sitemap.xmlController):

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activesupport (7.0.3) lib/active_support/inflector/methods.rb:280:in `constantize'
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railties (7.0.3) lib/rails/rack/logger.rb:40:in `call_app'
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rack (2.2.7) lib/rack/method_override.rb:24:in `call'
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rack (2.2.7) lib/rack/runtime.rb:22:in `call'
newrelic_rpm (9.2.2) lib/new_relic/agent/instrumentation/middleware_tracing.rb:99:in `call'
activesupport (7.0.3) lib/active_support/cache/strategy/local_cache_middleware.rb:29:in `call'
newrelic_rpm (9.2.2) lib/new_relic/agent/instrumentation/middleware_tracing.rb:99:in `call'
actionpack (7.0.3) lib/action_dispatch/middleware/executor.rb:14:in `call'
newrelic_rpm (9.2.2) lib/new_relic/agent/instrumentation/middleware_tracing.rb:99:in `call'
rack (2.2.7) lib/rack/sendfile.rb:110:in `call'
newrelic_rpm (9.2.2) lib/new_relic/agent/instrumentation/middleware_tracing.rb:99:in `call'
actionpack (7.0.3) lib/action_dispatch/middleware/host_authorization.rb:131:in `call'
newrelic_rpm (9.2.2) lib/new_relic/agent/instrumentation/middleware_tracing.rb:99:in `call'
rack-mini-profiler (3.1.0) lib/mini_profiler.rb:260:in `call'
newrelic_rpm (9.2.2) lib/new_relic/agent/instrumentation/middleware_tracing.rb:99:in `call'
railties (7.0.3) lib/rails/engine.rb:530:in `call'
railties (7.0.3) lib/rails/railtie.rb:226:in `public_send'
railties (7.0.3) lib/rails/railtie.rb:226:in `method_missing'
newrelic_rpm (9.2.2) lib/new_relic/agent/instrumentation/middleware_tracing.rb:99:in `call'
/usr/share/ruby/vendor_ruby/phusion_passenger/rack/thread_handler_extension.rb:107:in `process_request'
/usr/share/ruby/vendor_ruby/phusion_passenger/request_handler/thread_handler.rb:149:in `accept_and_process_next_request'
/usr/share/ruby/vendor_ruby/phusion_passenger/request_handler/thread_handler.rb:110:in `main_loop'
/usr/share/ruby/vendor_ruby/phusion_passenger/request_handler.rb:419:in `block (3 levels) in start_threads'
/usr/share/ruby/vendor_ruby/phusion_passenger/utils.rb:113:in `block in create_thread_and_abort_on_exception'
newrelic_rpm (9.2.2) lib/new_relic/agent/tracer.rb:434:in `block (2 levels) in thread_block_with_current_transaction'
newrelic_rpm (9.2.2) lib/new_relic/agent/tracer.rb:356:in `capture_segment_error'
newrelic_rpm (9.2.2) lib/new_relic/agent/tracer.rb:433:in `block in thread_block_with_current_transaction'

[syphax-bouazzouni]

hello @fillies,

You can remove the /var/log/messages, /var/log/httpd/error_log, as they are not useful in this case.

For /srv/ontoportal/ontologies_api/shared/log/unicorn.stderr.log it should not be empty. Try to check maybe /srv/ontoportal/ontologies_api/current/log/unicorn.stderr.log and /srv/ontoportal/ontologies_api/current/log/appliance.log

The /var/log/rails/appliance.log, is good, but shows the wrong error. The part of the log that you shared, shows an error in the homepage (by this line /releases/20220602203400/app/controllers/home_controller.rb:5:in 'index' ), you should search for something like this: /app/controllers/concept_controller.rb:5:in 'show' that does the display of the tree children (in the code this https://github.com/biodivportal/ontoportal_web_ui/blob/master/app/controllers/concepts_controller.rb#L30)

Have you experienced this issue with other Ontologies? or only related to ITIS as it is a big resource

[fillies]

Hello @syphax-bouazzouni,

thank you for your quick response! I removed the unuseful logs. And added some for /srv/ontoportal/ontologies_api/shared/log/unicorn.stderr.log. It sadly seems that /var/log/rails/appliance.log has not been updated since last year. Therefore, not displaying the error. But there was a pointer set to srv/ontoportal/bioportal_web_ui/shared/log/ which has been updated and contains an error regarding at least the ontologies_controler. I attach it above.

The Error persist also in other ontologies: Link But I do think it has to do with the size and the set timeout.

Thank you very much.

[naouelkaram]

Errors when I try to display the hierarchy: https://biodivportal.gfbio.org/ontologies/BOHLMANN/?p=classes

https://biodivportal.gfbio.org/ontologies/IOC/?p=classes

With 50K and 10K concepts