search

ncbo / bioportal_web_ui

A Rails application for biological ontologies
http://bioportal.bioontology.org/
Other
21 stars 2 forks source link

Improve accessing ontologies without submissions #227

Open alexskr opened 1 year ago

alexskr commented 1 year ago

UI doesn't gracefully handle accessing ontologies without submissions. Even though users might not see errors (unless they view the page with developer tools enabled in the browser) UI and API logs ERROR.
Ideally, UI should not make a bunch of API calls which would fail for ontologies that do not have any submissions

UI:

F, [2022-11-02T12:04:41.946626 #9934] FATAL -- : [d0b5e91b-54d6-4113-b0e4-28eff36ba58b]
[d0b5e91b-54d6-4113-b0e4-28eff36ba58b] ActiveRecord::RecordNotFound (Not Found):
[d0b5e91b-54d6-4113-b0e4-28eff36ba58b]
[d0b5e91b-54d6-4113-b0e4-28eff36ba58b] app/controllers/application_controller.rb:91:in `not_found'
[d0b5e91b-54d6-4113-b0e4-28eff36ba58b] app/controllers/application_controller.rb:413:in `get_class'
[d0b5e91b-54d6-4113-b0e4-28eff36ba58b] app/controllers/ontologies_controller.rb:144:in `classes'
[d0b5e91b-54d6-4113-b0e4-28eff36ba58b] app/controllers/ontologies_controller.rb:301:in `show'
E, [2022-11-02T12:08:20.958856 #21724] ERROR -- : [0d3adbc7-e14d-4489-a01c-faf2d8d0c93e] No submissions for ontology: https://data.bioontology.org/ontologies/APPENDIX
F, [2022-11-02T12:08:22.203664 #9934] FATAL -- : [f5f7ce91-a81a-4f60-aee8-24fd9eb92d5f]
[f5f7ce91-a81a-4f60-aee8-24fd9eb92d5f] NoMethodError (undefined method `first' for nil:NilClass):
[f5f7ce91-a81a-4f60-aee8-24fd9eb92d5f]
[f5f7ce91-a81a-4f60-aee8-24fd9eb92d5f] app/controllers/application_controller.rb:400:in `get_class'
[f5f7ce91-a81a-4f60-aee8-24fd9eb92d5f] app/controllers/concepts_controller.rb:84:in `show_tree'
E, [2022-11-02T12:08:22.226937 #16903] ERROR -- : [31d0e721-665a-4455-94e7-17d07568f450] No submissions for ontology: https://data.bioontology.org/ontologies/APPENDIX
E, [2022-11-02T12:08:22.272683 #23768] ERROR -- : [018eb902-6070-4411-a9e7-8d778f70d347] No submissions for ontology: https://data.bioontology.org/ontologies/APPENDIX
E, [2022-11-02T12:08:22.277970 #23960] ERROR -- : [f622caa8-3861-464b-b7c5-d4d95881327e] No submissions for ontology: https://data.bioontology.org/ontologies/APPENDIX
E, [2022-11-02T12:08:22.290463 #21724] ERROR -- : [ab370dad-4f9e-4d45-a2f3-94ed125490f7] No submissions for ontology: https://data.bioontology.org/ontologies/APPENDIX
E, [2022-11-02T12:08:22.295847 #23802] ERROR -- : [01a80ca7-84d2-4c17-8937-5b5ca07560f2] No submissions for ontology: https://data.bioontology.org/ontologies/APPENDIX
F, [2022-11-02T12:08:22.374088 #16903] FATAL -- : [31d0e721-665a-4455-94e7-17d07568f450]
[31d0e721-665a-4455-94e7-17d07568f450] NoMethodError (undefined method `first' for nil:NilClass):
[31d0e721-665a-4455-94e7-17d07568f450]
[31d0e721-665a-4455-94e7-17d07568f450] app/controllers/application_controller.rb:400:in `get_class'
[31d0e721-665a-4455-94e7-17d07568f450] app/controllers/ontologies_controller.rb:144:in `classes'
[31d0e721-665a-4455-94e7-17d07568f450] app/controllers/ontologies_controller.rb:301:in `show'
F, [2022-11-02T12:08:22.426568 #23960] FATAL -- : [f622caa8-3861-464b-b7c5-d4d95881327e]
[f622caa8-3861-464b-b7c5-d4d95881327e] ActionView::Template::Error (undefined method `first' for nil:NilClass):
[f622caa8-3861-464b-b7c5-d4d95881327e]     134:                           %code uri
[f622caa8-3861-464b-b7c5-d4d95881327e]     135:                           put the complete URI of the class (e.g.,
[f622caa8-3861-464b-b7c5-d4d95881327e]     136:                           = succeed ")" do
[f622caa8-3861-464b-b7c5-d4d95881327e]     137:                             %a.external.free{:href => @ontology.explore.classes["collection"].first.id, :rel => "nofollow", :title => "/visualize/39478/Common_Neoplasm"}
[f622caa8-3861-464b-b7c5-d4d95881327e]     138:                               = @ontology.explore.classes["collection"].first.id
[f622caa8-3861-464b-b7c5-d4d95881327e]     139:                         %li
[f622caa8-3861-464b-b7c5-d4d95881327e]     140:                           %code shortid
[f622caa8-3861-464b-b7c5-d4d95881327e]
[f622caa8-3861-464b-b7c5-d4d95881327e] app/views/ontologies/_widgets.html.haml:137
[f622caa8-3861-464b-b7c5-d4d95881327e] app/views/ontologies/_widgets.html.haml:136
[f622caa8-3861-464b-b7c5-d4d95881327e] app/controllers/ontologies_controller.rb:385:in `widgets'
[f622caa8-3861-464b-b7c5-d4d95881327e] app/controllers/ontologies_controller.rb:310:in `show'
F, [2022-11-02T12:08:22.669836 #9934] FATAL -- : [5c7e9b64-f0e0-4553-aa15-1dbbe0db9675]
[5c7e9b64-f0e0-4553-aa15-1dbbe0db9675] NoMethodError (undefined method `first' for nil:NilClass):
[5c7e9b64-f0e0-4553-aa15-1dbbe0db9675]
[5c7e9b64-f0e0-4553-aa15-1dbbe0db9675] app/controllers/application_controller.rb:400:in `get_class'
[5c7e9b64-f0e0-4553-aa15-1dbbe0db9675] app/controllers/concepts_controller.rb:84:in `show_tree'
syphax-bouazzouni commented 1 year ago

It's funny because we resolved/discussed this issue just last week, see https://github.com/ontoportal-lirmm/bioportal_web_ui/issues/99

For now what we do at Agroportal is to hide the tabs classes, mappings, instances, schemes, collections,..., so that those calls are never sent.

For now, I can't really do a pull request about this small change because our two codes diverged too much. (see https://github.com/ncbo/bioportal_web_ui/pull/223)