Merge branch 'staging'

.simplecov

@@ -0,0 +1,52 @@
+APP_ROOT = Pathname.new(File.expand_path('..', __FILE__)).expand_path
+
+class AppRootFilter < SimpleCov::Filter
+  def matches?(source_file)
+    source_file.filename.sub(/^#{excluded_path.to_s}.*/, '').empty?
+  end
+
+  def excluded_path
+    APP_ROOT.join(filter_argument).expand_path
+  end
+end
+
+def app_root
+  Pathname.new(File.expand_path('../../', __FILE__))
+end
+
+def gemset_definition_file
+  rbenv = app_root.join('.rbenv-gemsets')
+  rbenv if rbenv.exist?
+end
+
+def gemsets
+  file = gemset_definition_file
+  if File.exist? file.to_s
+    file.readlines.map(&:strip).select { |line| !line.empty? }
+  else
+    []
+  end
+end
+
+if ENV['COVERAGE']
+  SimpleCov.start do
+    add_group "Controllers", "app/controllers"
+    add_group "FakeRecords", "app/fake_records"
+    add_group "Helpers",     "app/helpers"
+    add_group "Models",      "app/models"
+    add_group "Serializers", "app/serializers"
+    add_group "ViewHelpers", "app/viewhelpers"
+    add_group "Lib",         "lib"
+
+    add_filter AppRootFilter.new('config/')
+    add_filter AppRootFilter.new('spec/')
+    add_filter AppRootFilter.new('test/')
+
+    gemsets.each do |gemset|
+      add_filter AppRootFilter.new("#{gemset}/")
+    end
+
+    # Set timeout for merging coverage results to 30 minutes
+    merge_timeout(30 * 60)
+  end
+end

app/helpers/navigation_helper.rb

@@ -162,8 +162,6 @@ def ontology_nav_metadata
     [
       ['Projects', locid_for(resource, :projects),
        :projects],
-      ['Categories', locid_for(resource, :categories),
-       :categories],
       ['Tasks', locid_for(resource, :tasks),
        :tasks],
       ['License Models', locid_for(resource, :license_models),

app/models/hets_instance.rb

@@ -21,7 +21,7 @@ def initialize(msg = DEFAULT_MSG)
 
   STATES = %w(free force-free busy)
   MUTEX_KEY = :choose_hets_instance
-  FORCE_FREE_WAITING_PERIOD = 60.seconds
+  FORCE_FREE_WAITING_PERIOD = 1.days
 
   attr_accessible :name, :uri, :state, :queue_size
 
@@ -50,7 +50,12 @@ def initialize(msg = DEFAULT_MSG)
 
   def self.with_instance!
     instance = choose!
-    result = yield(instance)
+    begin
+      result = yield(instance)
+    rescue StandardError
+      Semaphore.exclusively(MUTEX_KEY) { instance.finish_work! }
+      raise
+    end
     Semaphore.exclusively(MUTEX_KEY) { instance.finish_work! }
     result
   end

app/models/proof_attempt.rb

@@ -8,6 +8,7 @@ class ProofAttempt < ActiveRecord::Base
   belongs_to :proof_status
   belongs_to :prover
   belongs_to :proof_attempt_configuration
+  has_one :axiom_selection, through: :proof_attempt_configuration
   has_one :prover_output
   has_one :tactic_script
   has_many :generated_axioms, dependent: :destroy

app/models/sine_axiom_selection.rb

@@ -24,7 +24,7 @@ def call
     Semaphore.exclusively(lock_key) do
       unless finished
         cleanup
-        preprocess
+        preprocess unless other_finished_sine_axiom_selections.any?
         select_axioms
         mark_as_finished!
       end
@@ -66,9 +66,8 @@ def calculate_commonness_table
 
   # Number of axioms in which the symbol occurs
   def calculate_commonness(symbol)
-    ssc = SineSymbolCommonness.
-      where(symbol_id: symbol.id,
-            axiom_selection_id: axiom_selection.id).first_or_initialize
+    ssc = sine_symbol_commonnesses.
+      where(symbol_id: symbol.id).first_or_initialize
     unless ssc.commonness
       ssc.commonness = query_commonness(symbol)
       ssc.save!
@@ -88,10 +87,9 @@ def calculate_symbol_axiom_trigger_table
   end
 
   def calculate_symbol_axiom_trigger(symbol, axiom)
-    ssat = SineSymbolAxiomTrigger.
+    ssat = sine_symbol_axiom_triggers.
       where(symbol_id: symbol.id,
-            axiom_id: axiom.id,
-            axiom_selection_id: axiom_selection.id).first_or_initialize
+            axiom_id: axiom.id).first_or_initialize
     unless ssat.tolerance
       ssat.tolerance = needed_tolerance(symbol, axiom)
       ssat.save!
@@ -113,6 +111,14 @@ def commonness_of_least_common_symbol(axiom)
     least_common_symbol(axiom).sine_symbol_commonness.commonness
   end
 
+  def other_finished_sine_axiom_selections
+    goal.proof_attempts.includes(:axiom_selection).map(&:axiom_selection).
+      select do |as|
+        as.specific.class == self.class && as.finished &&
+          as.id != axiom_selection.id
+      end.map(&:specific)
+  end
+
   def select_axioms
     @selected_axioms = triggered_axioms_by_commonness_threshold.to_a
     select_new_axioms(goal, 0)
@@ -123,7 +129,7 @@ def select_new_axioms(sentence, current_depth)
     return if depth_limit_reached?(current_depth)
     new_axioms = select_axioms_by_sentence(sentence) - @selected_axioms
     @selected_axioms += new_axioms
-    new_axioms.each { |axiom| select_new_axioms(axiom, current_depth + 1) }
+    new_axioms.each { |axiom| select_new_axioms(axiom, current_depth + 2) }
   end
 
   def select_axioms_by_sentence(sentence)

app/views/layouts/application.html.haml

@@ -17,6 +17,11 @@
       .container
         .row.flash-messages
           = flash_messages
+        .row.flash-messages
+          .alert.alert-info
+            Do you want to support the development of Ontohub by testing? Visit
+            = link_to 'test.ontohub.org', 'http://test.ontohub.org'
+            for more information
         .row
           - if cover_visible?
             = render partial: '/shared/cover'

app/views/ontologies/edit.html.haml

@@ -4,9 +4,6 @@
 
 = simple_form_for resource, url: resource_path(resource) do |f|
   = f.input :name, as: :string
-  = f.label :categories
-  .col-lg-10.well
-    = render partial: 'categories', locals: {hide_well: true}
   = f.input :ontology_type_id, collection: OntologyType.all
   = f.association :formality_level, collection: FormalityLevel.all, as: :radio_buttons
   = f.association :projects, collection: Project.all, as: :check_boxes

app/views/shared/_navbar.html.haml

@@ -17,7 +17,6 @@
         / For any visitor
         = menu_entry 'Repositories', :repositories
         = menu_entry Settings.OMS.pluralize.capitalize,   :ontologies
-        = menu_entry 'Categories',   :categories
         = menu_entry 'Symbols',      :symbols_search if !! Settings.display_symbols_tab
         = menu_entry 'Logics',       :logics
         = menu_entry 'Mappings',     :mappings

config/routes.rb

@@ -143,7 +143,7 @@
   # Subsites for ontologies
   ontology_subsites = %i(
     comments metadata graphs
-    projects categories tasks
+    projects tasks
   )
 
   ontology_api_subsites = %i(
@@ -536,7 +536,6 @@
 
   resources :mappings, only: :index
 
-  resources :categories, :only => [:index, :show]
   resources :projects
   resources :tasks
   resources :license_models
@@ -619,7 +618,6 @@
       resources :ontology_versions, :only => [:index, :show, :new, :create], :path => 'versions' do
         resource :oops_request, :only => [:show, :create]
       end
-      resources :categories
       resources :tasks
       resources :license_models
       resources :tools

db/migrate/20151022144003_add_index_on_sine_commonness.rb

@@ -0,0 +1,10 @@
+class AddIndexOnSineCommonness < ActiveRecord::Migration
+  def change
+    # We only want to send queries like
+    # SELECT "symbols".*, "sine_symbol_commonnesses".*
+    #   FROM "symbols" LEFT OUTER JOIN "sine_symbol_commonnesses" ON "sine_symbol_commonnesses"."symbol_id" = "symbols"."id"
+    #   ORDER BY sine_symbol_commonnesses.commonness ASC LIMIT 1
+    # Thus, we also add an index on the commonness.
+    add_index :sine_symbol_commonnesses, :commonness
+  end
+end

doc/productive_deployment.md

@@ -402,11 +402,21 @@ Start the git daemon:
 
 If there's a new version on http://www.elasticsearch.org/download/, just replace the version number.
 
-    sudo apt-get update
-    sudo apt-get install openjdk-7-jre-headless -y
-    wget https://download.elasticsearch.org/elasticsearch/elasticsearch/elasticsearch-1.4.1.deb
-    sudo dpkg -i elasticsearch-1.4.1.deb
-    sudo service elasticsearch start
+    + apt-get update
+    + apt-get install openjdk-7-jre-headless -y
+    wget https://download.elasticsearch.org/elasticsearch/elasticsearch/elasticsearch-1.7.3.deb
+
+Before you can start Elasticsearch you need to replace the `elasticsearch` user with the `esearch` user. Thats because there are only 8-character-accounts on our machines allowed. To do this you need to
+
+    + dpkg --unpack elasticsearch-1.7.3.deb
+    + sed -r -e '/^#?ES_(USER|GROUP)=/ { s,^#,, ; s,=.*,=esearch, }'  -i /etc/default/elasticsearch.dpkg-new
+    + sed -e '/rmdir/ s,$, || true,' -i /var/lib/dpkg/info/elasticsearch.postrm
+    + dpkg --configure elasticsearch
+    + update-rc.d elasticsearch defaults 95 10
+
+Afterwards you can start it with
+
+    + service elasticsearch start
 
 If you want to test it, you can do
 

features/support/env.rb

@@ -3,8 +3,7 @@
 # newer version of cucumber-rails. Consider adding your own code to a new file
 # instead of editing this one. Cucumber will automatically load all features/**/*.rb
 # files.
-require File.expand_path("../../../spec/shared_helper", __FILE__)
-
+require 'simplecov'
 require 'sidekiq/testing'
 require 'cucumber/rails'
 require 'capybara/poltergeist'

spec/models/hets_instance_spec.rb

@@ -71,6 +71,28 @@
                      headers: {}})
       end
 
+      context 'error on execution' do
+        let!(:hets_instance) { create :hets_instance, state: 'free' }
+
+        it 're-raises the error' do
+          expect do
+            HetsInstance.with_instance! { raise 'my_error' }
+          end.to raise_error('my_error')
+        end
+
+        it 'frees the instance' do
+          chosen = nil
+          begin
+            HetsInstance.with_instance! do |instance|
+              chosen = instance
+              raise 'my_error'
+            end
+          rescue StandardError
+            expect(chosen.state).to eq('free')
+          end
+        end
+      end
+
       context 'free, force-free and busy are available' do
         let!(:free) { create :hets_instance, state: 'free' }
         let!(:force_free) { create :hets_instance, state: 'force-free' }

spec/models/sine_axiom_selection_spec.rb

@@ -97,7 +97,7 @@
     end
   end
 
-  context 'parameter influence' do
+  context 'calling SInE' do
     setup_hets
     let(:repository) { create :repository }
 
@@ -130,6 +130,33 @@
       pac
     end
 
+    context 'not preprocessing if already preprocessed once' do
+      let(:proof_attempt_previous) { create :proof_attempt, theorem: theorem }
+      let(:sine_axiom_selection_previous) { create :sine_axiom_selection }
+      let!(:proof_attempt_configuration_previous) do
+        pac = proof_attempt.proof_attempt_configuration
+        pac.axiom_selection = subject.axiom_selection
+        sine_axiom_selection_previous.axiom_selection.
+          proof_attempt_configurations = [pac]
+        pac
+      end
+
+      before do
+        sine_axiom_selection_previous.call
+        allow(subject).to receive(:preprocess).and_call_original
+      end
+
+      it 'not calling preprocess' do
+        subject.call
+        expect(subject).not_to have_received(:preprocess)
+      end
+
+      it 'selecting axioms anyway' do
+        subject.call
+        expect(subject.axioms).not_to be_empty
+      end
+    end
+
     context 'commonness threshold' do
       context '0' do
         before do

spec/spec_helper.rb

@@ -1,11 +1,7 @@
 # This file is copied to spec/ when you run 'rails generate rspec:install'
 ENV["RAILS_ENV"] ||= 'test'
 
-require File.expand_path("../../spec/shared_helper", __FILE__)
-
-include SharedHelper
-use_simplecov if ENV['COVERAGE']
-
+require 'simplecov'
 require File.expand_path("../../config/environment", __FILE__)
 require File.expand_path("../hets_helper", __FILE__)
 require 'rspec/rails'