Upgrade ontologies_api_client library

Gemfile

@@ -57,7 +57,7 @@ gem 'iso-639', '~> 0.3.6'
 gem 'multi_json'
 gem 'mysql2', '0.5.5'
 gem 'oj'
-gem 'ontologies_api_client', github: 'ncbo/ontologies_api_ruby_client', tag: 'v2.3.0'
+gem 'ontologies_api_client', github: 'ncbo/ontologies_api_ruby_client', tag: 'v2.4.0'
 gem 'open_uri_redirections'
 gem 'pry'
 gem 'psych', '< 4'

Gemfile.lock

@@ -1,9 +1,9 @@
 GIT
   remote: https://github.com/ncbo/ontologies_api_ruby_client.git
-  revision: 027c749f5de3f644b0392197e9482be51738cbe8
-  tag: v2.3.0
+  revision: f589b13dfbbc133ea67cbae1a8f92b41ea85c14b
+  tag: v2.4.0
   specs:
-    ontologies_api_client (2.2.5)
+    ontologies_api_client (2.4.0)
       activesupport (= 7.0.8)
       addressable (~> 2.8)
       excon
@@ -13,7 +13,6 @@ GIT
       lz4-ruby
       multi_json
       oj
-      spawnling (= 2.1.5)
 
 GEM
   remote: https://rubygems.org/
@@ -352,7 +351,6 @@ GEM
       tilt
     select2-rails (4.0.13)
     sexp_processor (4.17.0)
-    spawnling (2.1.5)
     sprockets (4.2.1)
       concurrent-ruby (~> 1.0)
       rack (>= 2.2.4, < 4)

app/controllers/ontologies_controller.rb

@@ -188,7 +188,7 @@ def create
 
   def edit
     # Note: find_by_acronym includes ontology views
-    @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:id]).first
+    @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:id], include: 'all').first
     redirect_to_home unless session[:user] && @ontology.administeredBy.include?(session[:user].id) || session[:user].admin?
     @categories = LinkedData::Client::Models::Category.all
     @user_select_list = LinkedData::Client::Models::User.all.map {|u| [u.username, u.id]}
@@ -254,9 +254,9 @@ def show
     end
 
     # Note: find_by_acronym includes ontology views
-    @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first
+    @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology], include: 'all').first
     not_found if @ontology.nil?
-    
+
     # Handle the case where an ontology is converted to summary only. 
     # See: https://github.com/ncbo/bioportal_web_ui/issues/133.
     if @ontology.summaryOnly && params[:p].present?
@@ -313,7 +313,7 @@ def show
   end
 
   def submit_success
-    @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:id]).first
+    @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:id], include: 'all').first
     render 'submit_success'
   end
 
@@ -345,9 +345,9 @@ def update
       return
     end
     # Note: find_by_acronym includes ontology views
-    @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology][:acronym] || params[:id]).first
+    @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:id]).first
     @ontology.update_from_params(ontology_params)
-    error_response = @ontology.update
+    error_response = @ontology.update(cache_refresh_all: false)
     if response_error?(error_response)
       @categories = LinkedData::Client::Models::Category.all
       @user_select_list = LinkedData::Client::Models::User.all.map {|u| [u.username, u.id]}

app/controllers/projects_controller.rb

@@ -17,18 +17,11 @@ def index
   end
 
   def show
-    projects = LinkedData::Client::Models::Project.find_by_acronym(params[:id])
-    if projects.blank?
-      flash.alert = "Project not found: #{params[:id]}"
-      redirect_to projects_path
-      return
-    end
-
-    @project = projects.first
+    @project = LinkedData::Client::Models::Project.get(params[:id])
     @ontologies_used = []
     onts_used = @project.ontologyUsed
     onts_used.each do |ont_used|
-      ont = LinkedData::Client::Models::Ontology.find(ont_used)
+      ont = LinkedData::Client::Models::Ontology.get(ont_used, include: 'name,acronym')
       @ontologies_used << Hash['name', ont.name, 'acronym', ont.acronym] unless ont.nil?
     end
     @ontologies_used.sort_by! { |o| o['name'].downcase }
@@ -45,13 +38,7 @@ def new
   end
 
   def edit
-    projects = LinkedData::Client::Models::Project.find_by_acronym(params[:id])
-    if projects.blank?
-      flash.alert = "Project not found: #{params[:id]}"
-      redirect_to projects_path
-      return
-    end
-    @project = projects.first
+    @project = LinkedData::Client::Models::Project.get(params[:id])
     @user_select_list = LinkedData::Client::Models::User.all.map { |u| [u.username, u.id] }
     @user_select_list.sort! { |a, b| a[1].downcase <=> b[1].downcase }
     @usedOntologies = @project.ontologyUsed || []
@@ -84,21 +71,15 @@ def create
   end
 
   def update
-    projects = LinkedData::Client::Models::Project.find_by_acronym(params[:id])
-    if projects.blank?
-      flash.alert = "Project not found: #{params[:id]}"
-      redirect_to projects_path
-      return
-    end
-    @project = projects.first
+    @project = LinkedData::Client::Models::Project.get(params[:id])
     @project.update_from_params(project_params)
-    @user_select_list = LinkedData::Client::Models::User.all.map { |u| [u.username, u.id] }
-    @user_select_list.sort! { |a, b| a[1].downcase <=> b[1].downcase }
-    @usedOntologies = @project.ontologyUsed || []
-    @ontologies = LinkedData::Client::Models::Ontology.all
-    error_response = @project.update
+    error_response = @project.update(cache_refresh_all: false)
     if response_error?(error_response)
       @errors = response_errors(error_response)
+      @user_select_list = LinkedData::Client::Models::User.all.map { |u| [u.username, u.id] }
+      @user_select_list.sort! { |a, b| a[1].downcase <=> b[1].downcase }
+      @usedOntologies = @project.ontologyUsed || []
+      @ontologies = LinkedData::Client::Models::Ontology.all
       render :edit
     else
       flash[:notice] = 'Project successfully updated'
@@ -107,13 +88,7 @@ def update
   end
 
   def destroy
-    projects = LinkedData::Client::Models::Project.find_by_acronym(params[:id])
-    if projects.blank?
-      flash.alert = "Project not found: #{params[:id]}"
-      redirect_to projects_path
-      return
-    end
-    @project = projects.first
+    @project = LinkedData::Client::Models::Project.get(params[:id])
     error_response = @project.delete
     if response_error?(error_response)
       @errors = response_errors(error_response)

app/controllers/submissions_controller.rb

@@ -5,15 +5,8 @@ class SubmissionsController < ApplicationController
   before_action :authorize_and_redirect, only: [:edit, :update, :create, :new]
 
   def new
-    begin
-      # REVIEW: do we really need this double attempt to locate an ontology? I think find_by_acronym (below) should
-      #    be sufficient. It's not evident that we call the new method with a full URI anymore.
-      @ontology = LinkedData::Client::Models::Ontology.get(CGI.unescape(params[:ontology_id]))
-    rescue MultiJson::ParseError
-      nil
-    end
-
-    @ontology ||= LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id]).first
+    # NOTE: find_by_acronym includes ontology views
+    @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology_id]).first
     @submission = @ontology.explore.latest_submission
     @submission ||= LinkedData::Client::Models::OntologySubmission.new
   end

app/controllers/users_controller.rb

@@ -16,11 +16,7 @@ def index
   end
 
   def show
-    @user = if session[:user].admin? && params.has_key?(:id)
-              LinkedData::Client::Models::User.find_by_username(params[:id]).first
-            else
-              LinkedData::Client::Models::User.find(session[:user].id)
-            end
+    @user = LinkedData::Client::Models::User.get(params[:id], include: 'all')
     @all_ontologies = LinkedData::Client::Models::Ontology.all(ignore_custom_ontologies: true)
     @user_ontologies = @user.customOntology
 
@@ -41,8 +37,7 @@ def new
   end
 
   def edit
-    @user = LinkedData::Client::Models::User.find(params[:id])
-    @user ||= LinkedData::Client::Models::User.find_by_username(params[:id]).first
+    @user = LinkedData::Client::Models::User.get(params[:id], include: 'all')
   end
 
   def create
@@ -58,16 +53,15 @@ def create
       else
         flash[:notice] = 'Account was successfully created'
         session[:user] = LinkedData::Client::Models::User.authenticate(@user.username, @user.password)
-        redirect_to_browse
+        redirect_to user_path(@user.username)
       end
     else
       render 'new'
     end
   end
 
   def update
-    @user = LinkedData::Client::Models::User.find(params[:id])
-    @user = LinkedData::Client::Models::User.find_by_username(params[:id]).first if @user.nil?
+    @user = LinkedData::Client::Models::User.get(params[:id], include: 'all')
 
     @errors = validate_update(user_params)
     if @errors.empty?
@@ -78,7 +72,7 @@ def update
       end
 
       @user.update_from_params(user_params.merge!(role: user_roles))
-      error_response = @user.update
+      error_response = @user.update(cache_refresh_all: false)
 
       if response_error?(error_response)
         @errors = response_errors(error_response)
@@ -99,12 +93,10 @@ def update
 
   def destroy
     response = { errors: String.new(''), success: String.new('') }
-    @user = LinkedData::Client::Models::User.find(params[:id])
-    @user = LinkedData::Client::Models::User.find_by_username(params[:id]).first if @user.nil?
+    @user = LinkedData::Client::Models::User.get(params[:id])
     if session[:user].admin?
       @user.delete
       response[:success] << 'User deleted successfully '
-
     else
       response[:errors] << 'Not permitted '
     end

app/helpers/application_helper.rb

@@ -38,9 +38,7 @@ def clean_id(string)
   end
 
   def get_username(user_id)
-    user = LinkedData::Client::Models::User.find(user_id)
-    username = user.nil? ? user_id : user.username
-    username
+    user_id.split('/').last
   end
 
   def current_user_admin?