deprecate LEGACY_REST_URL variable

[alexskr]

According to the sample config file LEGACY_REST_URL is 'Legacy REST core service address (BioPortal v3.x and lower)'
BioPortal v3.x rest service was deprecated a while ago but this variable still in use:

bioportal_web_ui/app/controllers/ajax_proxy_controller.rb

Line 28 in b33ca41

url = URI.parse($LEGACY_REST_URL + params[:path])

bioportal_web_ui/lib/log.rb

Line 30 in 6f1fb33

log = RestClient::Resource.new $LEGACY_REST_URL + "/log", :timeout => 30

[syphax-bouazzouni]

In addition, there are 3 more places where it's used, see the screenshot below.

[alexskr]

flexviz is another deprecated adobe flash based visualization which needs to be purged as well

[alexskr]

can we remove these files?

https://github.com/ncbo/bioportal_web_ui/blob/6f1fb336eb27e57c444750c6c187bf23cc60a3b8/app/views/concepts/_software.html.erb
https://github.com/ncbo/bioportal_web_ui/blob/6f1fb336eb27e57c444750c6c187bf23cc60a3b8/app/views/concepts/_images.rhtmlold
https://github.com/ncbo/bioportal_web_ui/blob/6f1fb336eb27e57c444750c6c187bf23cc60a3b8/app/views/concepts/_flexviz.html.erb
https://github.com/ncbo/bioportal_web_ui/blob/6f1fb336eb27e57c444750c6c187bf23cc60a3b8/app/views/concepts/_images.html.erb

[syphax-bouazzouni]

in addition (two), the LEGACY_REST_URL is called in jsonp and remote methods, where they themselves are not used anywhere.

jsonp

remote

remote is called inside

bioportal_web_ui/lib/log.rb

Line 14 in 6f1fb33

def self.add(level, message, request = nil, remote_params = nil)

But will never be called because the add function is called nowhere in the code with request argument

my (personnel) conclusion

• we can remove jsonp and its route
• we can remove remote and its call in add
• we can also remove $REMOTE_LOGGING in the sample config file, because it was only used in remote

[syphax-bouazzouni]

Finally, I have some time ago a list of the unused view (that you can see below), stay to list all the related unused code to these views, and have a second verification of another person.

• List of unused views/code #219

[alexskr]

If i understand this correctly log.rb includes remote logging functionality if we set REMOTE_LOGGING. It was previously used for UI to log events to obsolete/non-existing v3 rest API. I think this can be safely removed.

[jvendetti]

I wasn't able to look at all 37 of the view templates that are listed as unused, but at first glance there are at least a few that are still employed by BioPortal.

layouts/angular.html.erb

This is the layout used by the ontology Browse page:

Started GET "/ontologies" for 127.0.0.1 at 2022-09-07 10:52:24 -0700
Processing by OntologiesController#index as HTML
  Rendering ontologies/browse.html.erb within layouts/angular

layouts/_ontology.html.haml

This layout is referenced inside of the virtual_show method in the notes controller:

bioportal_web_ui/app/controllers/notes_controller.rb

Line 35 in 6f1fb33

render :partial => 'list', :layout => 'ontology'

The method can be triggered by navigating to the top-level Notes tab for any ontology with notes, then clicking on any note subject:

Started GET "/ontologies/BRO/notes/https%3A%2F%2Fdata.bioontology.org%2Fnotes%2Fa5809cba-e4dd-4553-9b24-c010f9d27b50" for 127.0.0.1 at 2022-09-07 14:19:57 -0700
Processing by NotesController#virtual_show as */*
  Parameters: {"ontology"=>"BRO", "noteid"=>"https://data.bioontology.org/notes/a5809cba-e4dd-4553-9b24-c010f9d27b50"}
  Rendered notes/_thread.html.haml (Duration: 1610.9ms | Allocations: 3108739)
Completed 200 OK in 15722ms (Views: 1611.3ms | ActiveRecord: 0.0ms | Allocations: 3473884)

... though it wasn't immediately clear what would trigger the elseif and else clauses inside this method that reference the ontology layout partial.

application/_footer_appliance.html.haml

Used to render a different footer when running the application in appliance mode:

bioportal_web_ui/app/views/layouts/appliance.html.haml

Line 35 in 6f1fb33

= render partial: "footer_appliance"

notes/_list.html.haml

Used to render the notes associated with a particular class:

Started GET "/ajax_concepts/BRO/?conceptid=http%3A%2F%2Fbioontology.org%2Fontologies%2FResearchArea.owl%23Area_of_Research&callback=load" for 127.0.0.1 at 2022-09-07 14:00:14 -0700
Processing by ConceptsController#show as */*
  Parameters: {"conceptid"=>"http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research", "callback"=>"load", "ontology"=>"BRO"}
  Ontology Load (0.3ms)  SELECT `ontologies`.* FROM `ontologies` WHERE `ontologies`.`acronym` = 'BRO' LIMIT 1
  ↳ app/helpers/application_helper.rb:367:in `ontolobridge_instructions_template'
  Rendered concepts/_biomixer.html.erb (Duration: 0.1ms | Allocations: 42)
  Rendered concepts/_details.html.haml (Duration: 775.1ms | Allocations: 7617)
  Rendered notes/_list.html.haml (Duration: 6957.3ms | Allocations: 363722)

[syphax-bouazzouni]

layouts/angular.html.erb

This is the layout used by the ontology Browse page:

Started GET "/ontologies" for 127.0.0.1 at 2022-09-07 10:52:24 -0700
Processing by OntologiesController#index as HTML
  Rendering ontologies/browse.html.erb within layouts/angular

Yeah, for the angular layout indeed it is used, I don't remember why I listed it in my notes. Maybe just to remember to remove angular-js and update the browse page.

layouts/_ontology.html.haml

This layout is referenced inside of the virtual_show method in the notes controller:

bioportal_web_ui/app/controllers/notes_controller.rb

Line 35 in 6f1fb33

render :partial => 'list', :layout => 'ontology'

The method can be triggered by navigating to the top-level Notes tab for any ontology with notes, then clicking on any note subject:

Started GET "/ontologies/BRO/notes/https%3A%2F%2Fdata.bioontology.org%2Fnotes%2Fa5809cba-e4dd-4553-9b24-c010f9d27b50" for 127.0.0.1 at 2022-09-07 14:19:57 -0700
Processing by NotesController#virtual_show as */*
  Parameters: {"ontology"=>"BRO", "noteid"=>"https://data.bioontology.org/notes/a5809cba-e4dd-4553-9b24-c010f9d27b50"}
  Rendered notes/_thread.html.haml (Duration: 1610.9ms | Allocations: 3108739)
Completed 200 OK in 15722ms (Views: 1611.3ms | ActiveRecord: 0.0ms | Allocations: 3473884)

... though it wasn't immediately clear what would trigger the elseif and else clauses inside this method that reference the ontology layout partial.

Yes, but I think that the elseif and else clauses inside will never be fulfilled (not 100% sure)

application/_footer_appliance.html.haml

Used to render a different footer when running the application in appliance mode:

bioportal_web_ui/app/views/layouts/appliance.html.haml

Line 35 in 6f1fb33

= render partial: "footer_appliance"

Ah yes, i found that its only our local code that does no more is it.

notes/_list.html.haml

Used to render the notes associated with a particular class:

Started GET "/ajax_concepts/BRO/?conceptid=http%3A%2F%2Fbioontology.org%2Fontologies%2FResearchArea.owl%23Area_of_Research&callback=load" for 127.0.0.1 at 2022-09-07 14:00:14 -0700
Processing by ConceptsController#show as */*
  Parameters: {"conceptid"=>"http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research", "callback"=>"load", "ontology"=>"BRO"}
  Ontology Load (0.3ms)  SELECT `ontologies`.* FROM `ontologies` WHERE `ontologies`.`acronym` = 'BRO' LIMIT 1
  ↳ app/helpers/application_helper.rb:367:in `ontolobridge_instructions_template'
  Rendered concepts/_biomixer.html.erb (Duration: 0.1ms | Allocations: 42)
  Rendered concepts/_details.html.haml (Duration: 775.1ms | Allocations: 7617)
  Rendered notes/_list.html.haml (Duration: 6957.3ms | Allocations: 363722)

Indeed,

I updated the list with your remarks, thanks @jvendetti.