Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] BioPortal AMI

Alex Skrenchuk alex.skrenchuk at stanford.edu
Thu Oct 15 17:32:42 PDT 2015


Hi Hyunsoo,

It looks like BioPortal Web UI can’t access backend (ontologies_api) running on the AMI.  Would you please verify that the backend is running?

You can do so by going to the API  which runs on port 8080.
You should see something like:
{
·         -
"links": {
o    "submissions": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/submissions"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/submissions>,
o    "recommender_v1": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/recommender_v1"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/recommender_v1>,
o    "provisional_classes": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/provisional_classes"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/provisional_classes>,
o    "categories": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/categories"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/categories>,
o    "slices": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/slices"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/slices>,
o    "users": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/users"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/users>,
o    "projects": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/projects"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/projects>,
o    "metrics": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/metrics"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/metrics>,
o    "ontologies": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/ontologies"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/ontologies>,
o    "reviews": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/reviews"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/reviews>,
o    "search": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/search"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/search>,
o    "annotator": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/annotator"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/annotator>,
o    "replies": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/replies"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/replies>,
o    "documentation": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/documentation"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/documentation>,
o    "mappings": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/mappings"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/mappings>,
o    "resource_index": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/resource_index"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/resource_index>,
o    "notes": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/notes"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/notes>,
o    "groups": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/groups"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/groups>,
o    "analytics": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/analytics"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/analytics>,
o    "recommender": "http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/recommender"<http://ec2-54-144-108-88.compute-1.amazonaws.com:8080/recommender>,
o    -
"@context": {
§  "submissions": "http://data.bioontology.org/metadata/OntologySubmission"<http://data.bioontology.org/metadata/OntologySubmission>,
§  "provisional_classes": "http://data.bioontology.org/metadata/ProvisionalClass"<http://data.bioontology.org/metadata/ProvisionalClass>,
§  "categories": "http://data.bioontology.org/metadata/Category"<http://data.bioontology.org/metadata/Category>,
§  "slices": "http://data.bioontology.org/metadata/Slice"<http://data.bioontology.org/metadata/Slice>,
§  "users": "http://data.bioontology.org/metadata/User"<http://data.bioontology.org/metadata/User>,
§  "projects": "http://data.bioontology.org/metadata/Project"<http://data.bioontology.org/metadata/Project>,
§  "metrics": "http://data.bioontology.org/metadata/Metrics"<http://data.bioontology.org/metadata/Metrics>,
§  "ontologies": "http://data.bioontology.org/metadata/Ontology"<http://data.bioontology.org/metadata/Ontology>,
§  "reviews": "http://data.bioontology.org/metadata/Review"<http://data.bioontology.org/metadata/Review>,
§  "replies": "http://data.bioontology.org/metadata/Reply"<http://data.bioontology.org/metadata/Reply>,
§  "mappings": "http://data.bioontology.org/metadata/Mapping"<http://data.bioontology.org/metadata/Mapping>,
§  "notes": "http://data.bioontology.org/metadata/Note"<http://data.bioontology.org/metadata/Note>,
§  "groups": "http://data.bioontology.org/metadata/Group"<http://data.bioontology.org/metadata/Group>
}
}
}

If you are getting an error then next step would be to restart BioPortal stack with bprestart command:

[ec2-user at ip-10-164-193-207 config]$ sudo /usr/local/bin/bprestart
Stopping ncbo_cron:                                        [  OK  ]
Stopping httpd:                                            [  OK  ]
Stopping memcached:                                        [  OK  ]
Stopping mysqld:                                           [  OK  ]
Stopping nginx:                                            [  OK  ]
Stopping unicorn:                                          [  OK  ]
                                                           [  OK  ]
Stopping 4s-httpd: Stopping slaves:pidfile is  2458
                                                           [  OK  ]
node_number hostname
0           localhost
  store_name     status
  ontologies_api stopped
Stopping 4s-boss:                                          [  OK  ]
Stopping redis-server annotator:                           [  OK  ]
Stopping redis-server goo_cache:                           [  OK  ]
Stopping redis-server http_cache:                          [  OK  ]
MSG-0001: mgrep is now in daemon mode, pid is 3235, all messages would be in file /var/log/message
                                                           [  OK  ]
Starting mysqld:                                           [  OK  ]
Starting 4s-boss:                                          [  OK  ]
success 4s-boss is running
Starting 4s-httpd:Starting stores ontologies_apinode_number hostname
0           localhost
  store_name     status
  ontologies_api running
                                                           [  OK  ]
success 4s-httpd is running
Starting redis-server:                                     [  OK  ]
Starting redis-server:                                     [  OK  ]
Starting redis-server:                                     [  OK  ]
Starting unicorn:
Starting nginx:                                            [  OK  ]
Starting memcached:                                        [  OK  ]
Starting httpd:                                            [  OK  ]


Let me know if that resolves the problem.

-Alex


From: Kim, Hyunsoo [mailto:HKim at jcvi.org]
Sent: Monday, October 12, 2015 1:30 PM
To: Alex Skrenchuk <alex.skrenchuk at stanford.edu>
Cc: support at bioontology.org
Subject: Re: BioPortal AMI

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20151016/9da7c014/attachment-0001.html>


More information about the bioontology-support mailing list