1620 deletion of child ontologies (#1748)

* Make removed child ontologies "not present".

* Scope default children association of acts_as_tree to present ontologies.

* Show only present ontologies of this file.

* Fix ontology factory.

* Add cucumber features.

* Fix restoring children.

* Fix restoring a child ontology.

* Add specs for restoring children.

* Really fix restoring a child ontology.

* Only save the ontology if it has changed or if it is a new record.

app/models/ontology/associations_and_attributes.rb

@@ -2,6 +2,12 @@ module Ontology::AssociationsAndAttributes
   extend ActiveSupport::Concern
 
   included do
+    acts_as_tree
+    # Add the scope "present: true" to the children association by acts_as_tree.
+    Ontology.reflect_on_association(:children).
+      options[:conditions] = {present: true}
+    has_many :all_children, class_name: Ontology.to_s, foreign_key: 'parent_id'
+
     belongs_to :language
     belongs_to :logic, counter_cache: true
     belongs_to :ontology_type

app/models/ontology/class_methods_and_scopes.rb

@@ -72,6 +72,10 @@ module Ontology::ClassMethodsAndScopes
     scope :state, ->(*states) do
       where state: states.map(&:to_s)
     end
+
+    scope :present, ->() do
+      where(present: true)
+    end
   end
 
   module ClassMethods

app/models/ontology/distributed.rb

@@ -2,8 +2,6 @@ module Ontology::Distributed
   extend ActiveSupport::Concern
 
   included do
-    acts_as_tree
-
     def self.homogeneous
       select_with_character_selector(HOMOGENEOUS_SELECTOR)
     end

app/models/ontology_version/parsing.rb

@@ -65,7 +65,7 @@ def retrieve_available_provers
 
   def update_states_for_self_and_children(state)
     update_state!(state)
-    ontology.children.each do |child|
+    ontology.reload.children.each do |child|
       child.versions.where(commit_oid: commit_oid).first.update_state!(state)
       child.versions.where(commit_oid: commit_oid).first.save!
     end

app/views/files/_show_dir.html.haml

@@ -20,9 +20,9 @@
         %tr{"data-id" => entry.index}
           - if i == 0
             %td.ontology{rowspan: entries.size}
-              - unless entry.dir? || entry.ontologies.empty?
+              - unless entry.dir? || entry.ontologies.present.empty?
                 %ul.ontology-list
-                  - entry.ontologies.each do |ontology|
+                  - entry.ontologies.present.each do |ontology|
                     %li.ontology-list-item
                       = fancy_link ontology
                       - if ontology.state=='failed'

app/views/files/_show_file.html.haml

@@ -35,9 +35,9 @@
               = f.button t('files.discard'), type: 'cancel', id: 'codemirror-btn-discard', class: 'btn btn-danger'
       = render partial: 'modal_discard'
     - unless resource.ontologies.empty?
-      %h4
+      %h4#ontology-list-headline
         Defining
-        = pluralize resource.ontologies.size, Settings.OMS
+        = pluralize resource.ontologies.present.count, Settings.OMS
       %ul.ontology-list
-        - resource.ontologies.each do |ontology|
+        - resource.ontologies.present.each do |ontology|
           %li= fancy_link ontology

features/RepositoryEditFile.feature

@@ -0,0 +1,24 @@
+Feature: RepositoryEditFile
+
+Scenario: View the Ontologies of the file (SingleOntology)
+  Given I have uploaded an ontology
+  When I visit the file view of the ontology
+  Then I should see all the file's ontologies
+
+Scenario: View the Ontologies of the file (DistributedOntology)
+  Given I have uploaded a distributed ontology
+  When I visit the file view of the ontology
+  Then I should see all the file's ontologies
+
+Scenario: View the Ontologies of the file (DistributedOntology with deleted children)
+  Given I have uploaded a distributed ontology
+  And Children of the ontology have been deleted
+  When I visit the file view of the ontology
+  Then I should see all the file's ontologies
+
+Scenario: View the Ontologies of the file (DistributedOntology with restored children)
+  Given I have uploaded a distributed ontology
+  And Children of the ontology have been deleted
+  And Children of the ontology have been restored
+  When I visit the file view of the ontology
+  Then I should see all the file's ontologies

features/RepositoryFileBrowser.feature

@@ -0,0 +1,23 @@
+Feature: RepositoryFileBrowser
+
+Scenario: SingleOntology Display
+  Given I have uploaded an ontology
+  When I visit the file browser of the ontology's repository
+  Then I should see the ontology's file
+  And I should see the ontlogy next to the ontology's file
+  And I should see no other ontologies next to the ontology's file
+
+Scenario: DistributedOntology Display
+  Given I have uploaded a distributed ontology
+  When I visit the file browser of the ontology's repository
+  Then I should see the ontology's file
+  And I should see the ontlogy and its children next to the ontology's file
+  And I should see no other ontologies next to the ontology's file
+
+Scenario: DistributedOntology with Deleted Children Display
+  Given I have uploaded a distributed ontology
+  And Children of the ontology have been deleted
+  When I visit the file browser of the ontology's repository
+  Then I should see the ontology's file
+  And I should see the ontlogy and its children next to the ontology's file
+  And I should see no other ontologies next to the ontology's file

features/step_definitions/ontology_search_steps.rb

@@ -1,7 +1,3 @@
-Given(/^there is an ontology$/) do
-  @ontology = FactoryGirl.create :ontology
-end
-
 When(/^I open the ontologies overview page$/) do
   visit ontologies_path
 end

features/step_definitions/ontology_state_steps.rb

@@ -1,5 +1,6 @@
-Given(/^There is an ontology$/) do
+Given(/^There is an ontology$/i) do
   @ontology = FactoryGirl.create :ontology
+  @ontology_version = @ontology.current_version
 end
 
 Given(/^there is an ontology with a "([^"]+)" version$/) do |state|

features/step_definitions/ontology_versions_steps.rb

@@ -1,9 +1,10 @@
-Given(/^there is a distributed ontology$/) do
+Given(/^there is a distributed ontology$/i) do
   @distributed_ontology = FactoryGirl.create :distributed_ontology, :with_versioned_children
   @ontology = @distributed_ontology
+  @ontology_version = @ontology.current_version
 end
 
-Given(/^there is an ontology file$/) do
+Given(/^there is an ontology file$/i) do
   repository = @ontology.repository
   user = repository.permissions.first.subject
   Tempfile.create('testfile') do |f|

features/step_definitions/repository_edit_file_steps.rb

@@ -0,0 +1,58 @@
+def build_version_for(ontology)
+  commit_oid = '1'*40
+  ontology.versions.build(
+    {commit_oid: commit_oid,
+     commit: FactoryGirl.create(:commit, commit_oid: commit_oid),
+     basepath: File.basepath(ontology.path),
+     file_extension: File.extname(ontology.path),
+     fast_parse: false},
+    {without_protection: true})
+end
+
+Given(/^I have uploaded a(.*) ontology$/) do |type|
+  steps %Q{
+  Given I have an account
+  And I am logged in
+  And there is a#{type} ontology
+  And I have permissions to edit the ontology
+  And there is an ontology file
+  }
+end
+
+Given(/^Children of the ontology have been deleted$/i) do
+  @deleted_child = @ontology.children.last
+  @deleted_child.present = false
+  @deleted_child.save!
+
+  build_version_for(@ontology).save!
+  @ontology.children.each do |child|
+    build_version_for(child).save!
+  end
+end
+
+Given(/^Children of the ontology have been restored$/i) do
+  @deleted_child.present =true
+  @deleted_child.save!
+
+  build_version_for(@ontology).save!
+  @ontology.children.each do |child|
+    build_version_for(child).save!
+  end
+end
+
+When(/^I visit the file view of the ontology$/i) do
+  # The request object does not contain a requested mime type, so we need to
+  # stub this.
+  allow_any_instance_of(FilesController).
+    to receive(:existing_file_requested_as_html?).
+    and_return(true)
+  visit repository_tree_path(@ontology.repository, path: @ontology.path)
+end
+
+Then(/^I should see all the file's ontologies$/i) do
+  # The file defines the DistributedOntolgy and its children.
+  number = 1 + @ontology.children.count
+
+  expect(page.find('#ontology-list-headline').text).to match(/\s+#{number}\s+/)
+  expect(page).to have_selector('ul.ontology-list > li', count: number)
+end

features/step_definitions/repository_file_browser_steps.rb

@@ -0,0 +1,38 @@
+When(/^I visit the file browser of the ontology's repository$/i) do
+  visit repository_tree_path(@ontology.repository)
+end
+
+Then(/^I should see the ontology's file$/i) do
+  file_cell_selector = 'table.file-table td.name'
+  expect(page).to have_selector(file_cell_selector, count: 1)
+  expect(find(file_cell_selector).
+    has_link?(@ontology.path, polymorphic_path(@ontology))).
+    to be(true)
+end
+
+Then(/^I should see the ontlogy next to the ontology's file$/i) do
+  ontology_cell_selector = 'table.file-table td.ontology ul.ontology-list'
+  expect(page).to have_selector(ontology_cell_selector, count: 1)
+  expect(find(ontology_cell_selector).
+    has_link?(@ontology.name, polymorphic_path(@ontology))).
+    to be(true)
+end
+
+Then(/^I should see no other ontologies next to the ontology's file$/i) do
+  ontology_cell_selector = 'table.file-table td.ontology ul.ontology-list'
+  expect(find(ontology_cell_selector)).
+    to have_selector('li', count: 1 + @ontology.children.count)
+end
+
+Then(/^I should see the ontlogy and its children next to the ontology's file$/i) do
+  ontology_cell_selector = 'table.file-table td.ontology ul.ontology-list'
+  expect(page).to have_selector(ontology_cell_selector, count: 1)
+  expect(find(ontology_cell_selector).
+    has_link?(@ontology.name, polymorphic_path(@ontology))).
+    to be(true)
+  @ontology.children.each do |child|
+    expect(find(ontology_cell_selector).
+      has_link?(child.name, polymorphic_path(child))).
+      to be(true)
+  end
+end

features/support/env.rb

@@ -7,6 +7,7 @@
 require 'sidekiq/testing'
 require 'cucumber/rails'
 require 'capybara/poltergeist'
+require 'cucumber/rspec/doubles'
 require 'webmock'
 require 'vcr'
 

lib/hets/dg/node_evaluation_helper.rb

@@ -39,19 +39,19 @@ def procure_child_ontology(internal_iri)
         child_locid = parent_ontology.locid_for_child(internal_iri)
 
         # find or create child-ontology by IRI
-        ontology = parent_ontology.children.find_with_locid(child_locid)
+        ontology = parent_ontology.all_children.find_with_locid(child_locid)
         if ontology.nil?
           options = {
             name: internal_iri,
             basepath: parent_ontology.basepath,
             file_extension: parent_ontology.file_extension,
             repository_id: parent_ontology.repository_id,
-            present: true,
           }
           ontology = SingleOntology.new(options, without_protection: true)
           parent_ontology.children << ontology
-          ontology.save!
         end
+        ontology.present = true
+        ontology.save! if ontology.changed? || !ontology.persisted?
 
         version = ontology.versions.build
         version.basepath = ontology.basepath
@@ -149,6 +149,16 @@ def update_ontologies_per_logic_count!(ontologies)
           Logic.reset_counters(logic_id, :ontologies)
         end
       end
+
+      def set_all_children_inactive_except(present_ontologies)
+        return if parent_ontology.nil?
+        parent_ontology.all_children.each do |child|
+          unless present_ontologies.include?(child.name)
+            child.present = false
+            child.save!
+          end
+        end
+      end
     end
   end
 end

lib/hets/dg/node_evaluator.rb

@@ -7,6 +7,7 @@ class NodeEvaluator < ConcurrentEvaluator
       attr_accessor :current_element
       attr_accessor :internal_iri
 
+      register :all, :start, to: :all_start
       register :all, :end, to: :all_end
       register :root, :start, to: :dgraph
       register :ontology, :start, to: :ontology_start
@@ -22,6 +23,10 @@ def dgraph(current_element)
         importer.dgnode_count = current_element['dgnodes'].to_i
       end
 
+      def all_start
+        @node_names = []
+      end
+
       def all_end
         importer.versions.compact.each do |version|
           version.save!
@@ -33,9 +38,11 @@ def all_end
           ontology.__elasticsearch__.index_document
           ontology.__elasticsearch__.update_document
         end
+        set_all_children_inactive_except(@node_names)
       end
 
       def ontology_start(current_element)
+        @node_names << current_element['name']
         self.internal_iri = child_name = current_element['name']
 
         ontohub_iri = generate_ontology_iri(internal_iri, current_element)

spec/factories/ontology_factory.rb

@@ -16,6 +16,7 @@
     description { Faker::Lorem.paragraph }
     logic { FactoryGirl.create :logic }
     state { 'pending' }
+    present { true }
 
     factory :done_ontology do
       state { 'done' }
@@ -119,11 +120,17 @@
 
           logic = FactoryGirl.create(:logic)
           child_one = FactoryGirl.build(:ontology, :with_version,
+            parent: ontology,
+            basepath: ontology.basepath,
+            file_extension: ontology.file_extension,
             logic: logic,
             repository: ontology.repository)
           child_one.versions.first.parent = version
 
           child_two = FactoryGirl.build(:ontology, :with_version,
+            parent: ontology,
+            basepath: ontology.basepath,
+            file_extension: ontology.file_extension,
             logic: logic,
             repository: ontology.repository)
           child_two.versions.first.parent = version
@@ -132,8 +139,6 @@
                             source: child_one,
                             target: child_two,
                             ontology: ontology)
-
-          ontology.children.push(child_one, child_two)
         end
       end
 

spec/fixtures/ontologies/casl/test2_child_deleted.casl

@@ -0,0 +1,8 @@
+spec sp =
+  sort s
+  op f:s->s
+  . forall x:s . f(x) = x
+then
+  . exists x:s . f(x) = x
+with s |-> s
+end

spec/fixtures/ontologies/casl/test2_child_renamed.casl

@@ -0,0 +1,12 @@
+spec sp =
+  sort s
+  op f:s->s
+  . forall x:s . f(x) = x
+then
+  . exists x:s . f(x) = x
+with s |-> s
+end
+
+spec sp1_renamed =
+  sp hide f
+end