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[bioontology-support] BioPortal AMI

Kim, Hyunsoo HKim at jcvi.org
Mon Oct 12 13:29:56 PDT 2015


Hi Alex,

1. I’m using m4.xlarge
2. I have not loaded any ontologies yet as I am having issues with accessing the homepage of Bioportal
3.
more /srv/ncbo/ontologies_api/current/log/production.log
127.0.0.1 - admin [12/Oct/2015:20:17:59 +0000] "PATCH /users/admin?apikey=1cfae05f-9e67-486f-820b-b39
3dec5764b HTTP/1.0" 204 - 1.5707

Thanks,
Hyunsoo

On Oct 9, 2015, at 9:13 PM, Alex Skrenchuk <alex.skrenchuk at stanford.edu<mailto:alex.skrenchuk at stanford.edu>> wrote:

Hi Kim,

Would you provide us more information on your NCBO Appliance AMI instance:

1.       What instance size did you select for the AMI?  Running NCBO Appliance on smaller instances such as m3.medium could be problematic.
2.       Have you loaded any ontologies into the appliance?
3.       Would you provide logs from the ontologies_api  (/srv/ncbo/ontologies_api/current/log/production.log)

Thanks,
Alex

From: bioontology-support [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Kim, Hyunsoo
Sent: Friday, October 09, 2015 8:21 AM
To: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] BioPortal AMI

Hello,

I have not header anything about my inquiry yet so am resending it.

Thanks,
Hyunsoo

On Oct 5, 2015, at 1:53 PM, Kim, Hyunsoo <HKim at jcvi.org<mailto:HKim at jcvi.org>> wrote:

Hello,

I am testing the AWS AMI for NCBO Bioportal, and the initialization process went smoothly. However, every request to the ncbo service fails with following error:

Started GET "/ontologies" for 192.207.234.194 at 2015-10-05 17:46:55 +0000
Processing by OntologiesController#index as HTML
Completed 500 Internal Server Error in 0.5ms

URI::InvalidURIError (Problem retrieving:
http://<?xml<http://%3c/?xml> version="1.0" encoding="iso-8859-1"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
         "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
 <head>
  <title>404 - Not Found</title>
 </head>
 <body>
  <h1>404 - Not Found</h1>
 </body>
</html>
:8080

Error: bad URI(is not URI?): http://<?xml<http://%3c/?xml> version="1.0" encoding="iso-8859-1"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
         "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
 <head>
  <title>404 - Not Found</title>
 </head>
 <body>
  <h1>404 - Not Found</h1>
 </body>
</html>
:8080
/usr/share/ruby/2.1/uri/common.rb:176:in `split'
/usr/share/ruby/2.1/uri/common.rb:211:in `parse'
/usr/share/ruby/2.1/uri/common.rb:747:in `parse'
/usr/share/ruby/2.1/uri/common.rb:1232:in `URI'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/faraday-0.9.1/lib/faraday/utils.rb:246:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/faraday-0.9.1/lib/faraday/utils.rb:246:in `URI'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/faraday-0.9.1/lib/faraday/connection.rb:309:in `url_prefix='
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/faraday-0.9.1/lib/faraday/connection.rb:77:in `initialize'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/faraday-0.9.1/lib/faraday.rb:70:in `new'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/faraday-0.9.1/lib/faraday.rb:70:in `new'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/bundler/gems/ontologies_api_ruby_client-dd22b45c3ade/lib/ontologies_api_client/config.rb:39:in `config_connection'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/bundler/gems/ontologies_api_ruby_client-dd22b45c3ade/lib/ontologies_api_client/http.rb:48:in `conn'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/bundler/gems/ontologies_api_ruby_client-dd22b45c3ade/lib/ontologies_api_client/http.rb:63:in `get'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/bundler/gems/ontologies_api_ruby_client-dd22b45c3ade/lib/ontologies_api_client/collection.rb:28:in `top_level_links'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/bundler/gems/ontologies_api_ruby_client-dd22b45c3ade/lib/ontologies_api_client/collection.rb:43:in `entry_point'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/bundler/gems/ontologies_api_ruby_client-dd22b45c3ade/lib/ontologies_api_client/collection.rb:56:in `all'
/srv/rails/BioPortal/releases/bioportal_web_ui/app/controllers/ontologies_controller.rb:45:in `index'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_controller/metal/implicit_render.rb:4:in `send_action'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/abstract_controller/base.rb:167:in `process_action'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_controller/metal/rendering.rb:10:in `process_action'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/abstract_controller/callbacks.rb:18:in `block in process_action'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activesupport-3.2.21/lib/active_support/callbacks.rb:458:in `_run__3587100991550631146__process_action__963253783299443448__callbacks'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activesupport-3.2.21/lib/active_support/callbacks.rb:405:in `__run_callback'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activesupport-3.2.21/lib/active_support/callbacks.rb:385:in `_run_process_action_callbacks'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activesupport-3.2.21/lib/active_support/callbacks.rb:81:in `run_callbacks'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/abstract_controller/callbacks.rb:17:in `process_action'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_controller/metal/rescue.rb:29:in `process_action'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_controller/metal/instrumentation.rb:30:in `block in process_action'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activesupport-3.2.21/lib/active_support/notifications.rb:123:in `block in instrument'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activesupport-3.2.21/lib/active_support/notifications/instrumenter.rb:20:in `instrument'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activesupport-3.2.21/lib/active_support/notifications.rb:123:in `instrument'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_controller/metal/instrumentation.rb:29:in `process_action'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_controller/metal/params_wrapper.rb:207:in `process_action'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activerecord-3.2.21/lib/active_record/railties/controller_runtime.rb:18:in `process_action'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/abstract_controller/base.rb:121:in `process'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/abstract_controller/rendering.rb:45:in `process'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/rack-mini-profiler-0.9.3/lib/mini_profiler/profiling_methods.rb:77:in `block in profile_method'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_controller/metal.rb:203:in `dispatch'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_controller/metal/rack_delegation.rb:14:in `dispatch'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_controller/metal.rb:246:in `block in action'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_dispatch/routing/route_set.rb:73:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_dispatch/routing/route_set.rb:73:in `dispatch'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_dispatch/routing/route_set.rb:36:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/journey-1.0.4/lib/journey/router.rb:68:in `block in call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/journey-1.0.4/lib/journey/router.rb:56:in `each'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/journey-1.0.4/lib/journey/router.rb:56:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_dispatch/routing/route_set.rb:608:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_dispatch/middleware/best_standards_support.rb:17:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/rack-1.4.5/lib/rack/etag.rb:23:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/rack-1.4.5/lib/rack/conditionalget.rb:25:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_dispatch/middleware/head.rb:14:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_dispatch/middleware/params_parser.rb:21:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_dispatch/middleware/flash.rb:242:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/rack-1.4.5/lib/rack/session/abstract/id.rb:210:in `context'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/rack-1.4.5/lib/rack/session/abstract/id.rb:205:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_dispatch/middleware/cookies.rb:341:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activerecord-3.2.21/lib/active_record/query_cache.rb:64:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activerecord-3.2.21/lib/active_record/connection_adapters/abstract/connection_pool.rb:479:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_dispatch/middleware/callbacks.rb:28:in `block in call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activesupport-3.2.21/lib/active_support/callbacks.rb:405:in `_run__2477054876280584018__call__3884238363076606039__callbacks'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activesupport-3.2.21/lib/active_support/callbacks.rb:405:in `__run_callback'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activesupport-3.2.21/lib/active_support/callbacks.rb:385:in `_run_call_callbacks'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activesupport-3.2.21/lib/active_support/callbacks.rb:81:in `run_callbacks'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_dispatch/middleware/callbacks.rb:27:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_dispatch/middleware/remote_ip.rb:31:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_dispatch/middleware/debug_exceptions.rb:16:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_dispatch/middleware/show_exceptions.rb:56:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/railties-3.2.21/lib/rails/rack/logger.rb:32:in `call_app'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/railties-3.2.21/lib/rails/rack/logger.rb:16:in `block in call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activesupport-3.2.21/lib/active_support/tagged_logging.rb:22:in `tagged'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/railties-3.2.21/lib/rails/rack/logger.rb:16:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/actionpack-3.2.21/lib/action_dispatch/middleware/request_id.rb:22:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/rack-1.4.5/lib/rack/methodoverride.rb:21:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/rack-1.4.5/lib/rack/runtime.rb:17:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/activesupport-3.2.21/lib/active_support/cache/strategy/local_cache.rb:72:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/rack-1.4.5/lib/rack/lock.rb:15:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/rack-cache-1.2/lib/rack/cache/context.rb:136:in `forward'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/rack-cache-1.2/lib/rack/cache/context.rb:245:in `fetch'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/rack-cache-1.2/lib/rack/cache/context.rb:185:in `lookup'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/rack-cache-1.2/lib/rack/cache/context.rb:66:in `call!'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/rack-cache-1.2/lib/rack/cache/context.rb:51:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/rack-mini-profiler-0.9.3/lib/mini_profiler/profiler.rb:167:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/railties-3.2.21/lib/rails/engine.rb:484:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/railties-3.2.21/lib/rails/application.rb:231:in `call'
/srv/rails/BioPortal/releases/bioportal_web_ui/vendor/bundle/ruby/2.1/gems/railties-3.2.21/lib/rails/railtie/configurable.rb:30:in `method_missing'
/usr/local/share/ruby/gems/2.1/gems/passenger-4.0.57/lib/phusion_passenger/rack/thread_handler_extension.rb:74:in `process_request'
/usr/local/share/ruby/gems/2.1/gems/passenger-4.0.57/lib/phusion_passenger/request_handler/thread_handler.rb:141:in `accept_and_process_next_request'
/usr/local/share/ruby/gems/2.1/gems/passenger-4.0.57/lib/phusion_passenger/request_handler/thread_handler.rb:109:in `main_loop'
/usr/local/share/ruby/gems/2.1/gems/passenger-4.0.57/lib/phusion_passenger/request_handler.rb:455:in `block (3 levels) in start_threads'):
  app/controllers/ontologies_controller.rb:45:in `index'

The page displays "We're sorry but something has gone wrong. We have been notified of this error.” message for the error. Where should I look into to fix this issue? Is there any detailed HOWTO guide for the AMI and services?

Additionally, how could I obtain the vmware virtual appliance? My BioPortal account is ‘hkim500’.

Thanks,
Hyunsoo

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