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[bioontology-support] BioPortal AMI

Alex Skrenchuk alex.skrenchuk at stanford.edu
Fri Oct 9 18:13:38 PDT 2015


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
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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