Support both internal and external issue trackers

31 files changed, 563 insertions, 99 deletions

diff --git a/app/controllers/projects/issues_controller.rb b/app/controllers/projects/issues_controller.rb
index 5b0eeac2477..e2ccabb22db 100644
--- a/app/controllers/projects/issues_controller.rb
+++ b/app/controllers/projects/issues_controller.rb
@@ -269,10 +269,6 @@ class Projects::IssuesController < Projects::ApplicationController
     end
   end
 
-  def module_enabled
-    render_404 unless @project.feature_available?(:issues, current_user)
-  end
-
   def issue_params
     params.require(:issue).permit(*issue_params_attributes)
   end
diff --git a/app/helpers/issues_helper.rb b/app/helpers/issues_helper.rb
index 42b6cfdf02f..7e1ccb23e9e 100644
--- a/app/helpers/issues_helper.rb
+++ b/app/helpers/issues_helper.rb
@@ -17,10 +17,10 @@ module IssuesHelper
     return '' if project.nil?
 
     url =
-      if options[:only_path]
-        project.issues_tracker.issue_path(issue_iid)
+      if options[:internal]
+        url_for_internal_issue(issue_iid, project, options)
       else
-        project.issues_tracker.issue_url(issue_iid)
+        url_for_tracker_issue(issue_iid, project, options)
       end
 
     # Ensure we return a valid URL to prevent possible XSS.
@@ -29,6 +29,24 @@ module IssuesHelper
     ''
   end
 
+  def url_for_tracker_issue(issue_iid, project, options)
+    if options[:only_path]
+      project.issues_tracker.issue_path(issue_iid)
+    else
+      project.issues_tracker.issue_url(issue_iid)
+    end
+  end
+
+  def url_for_internal_issue(issue_iid, project = @project, options = {})
+    helpers = Gitlab::Routing.url_helpers
+
+    if options[:only_path]
+      helpers.namespace_project_issue_path(namespace_id: project.namespace, project_id: project, id: issue_iid)
+    else
+      helpers.namespace_project_issue_url(namespace_id: project.namespace, project_id: project, id: issue_iid)
+    end
+  end
+
   def bulk_update_milestone_options
     milestones = @project.milestones.active.reorder(due_date: :asc, title: :asc).to_a
     milestones.unshift(Milestone::None)
@@ -158,4 +176,6 @@ module IssuesHelper
 
   # Required for Banzai::Filter::IssueReferenceFilter
   module_function :url_for_issue
+  module_function :url_for_internal_issue
+  module_function :url_for_tracker_issue
 end
diff --git a/app/models/merge_request.rb b/app/models/merge_request.rb
index e4e7999d0f2..a910099b4c1 100644
--- a/app/models/merge_request.rb
+++ b/app/models/merge_request.rb
@@ -596,7 +596,7 @@ class MergeRequest < ActiveRecord::Base
   # running `ReferenceExtractor` on each of them separately.
   # This optimization does not apply to issues from external sources.
   def cache_merge_request_closes_issues!(current_user)
-    return if project.has_external_issue_tracker?
+    return unless project.issues_enabled?
 
     transaction do
       self.merge_requests_closing_issues.delete_all
diff --git a/app/models/project.rb b/app/models/project.rb
index 0b357d5d003..d827bfaa806 100644
--- a/app/models/project.rb
+++ b/app/models/project.rb
@@ -734,9 +734,11 @@ class Project < ActiveRecord::Base
   end
 
   def get_issue(issue_id, current_user)
-    if default_issues_tracker?
-      IssuesFinder.new(current_user, project_id: id).find_by(iid: issue_id)
-    else
+    issue = IssuesFinder.new(current_user, project_id: id).find_by(iid: issue_id) if issues_enabled?
+
+    if issue
+      issue
+    elsif external_issue_tracker
       ExternalIssue.new(issue_id, self)
     end
   end
@@ -758,7 +760,7 @@ class Project < ActiveRecord::Base
   end
 
   def external_issue_reference_pattern
-    external_issue_tracker.class.reference_pattern
+    external_issue_tracker.class.reference_pattern(only_long: issues_enabled?)
   end
 
   def default_issues_tracker?
diff --git a/app/models/project_services/issue_tracker_service.rb b/app/models/project_services/issue_tracker_service.rb
index 6d6a3ae3647..31984c5d7ed 100644
--- a/app/models/project_services/issue_tracker_service.rb
+++ b/app/models/project_services/issue_tracker_service.rb
@@ -8,8 +8,12 @@ class IssueTrackerService < Service
   # This pattern does not support cross-project references
   # The other code assumes that this pattern is a superset of all
   # overriden patterns. See ReferenceRegexes::EXTERNAL_PATTERN
-  def self.reference_pattern
-    @reference_pattern ||= %r{(\b[A-Z][A-Z0-9_]+-|#{Issue.reference_prefix})(?<issue>\d+)}
+  def self.reference_pattern(only_long: false)
+    if only_long
+      %r{(\b[A-Z][A-Z0-9_]+-)(?<issue>\d+)}
+    else
+      %r{(\b[A-Z][A-Z0-9_]+-|#{Issue.reference_prefix})(?<issue>\d+)}
+    end
   end
 
   def default?
diff --git a/app/models/project_services/jira_service.rb b/app/models/project_services/jira_service.rb
index 5498a2e17b2..450027c2e57 100644
--- a/app/models/project_services/jira_service.rb
+++ b/app/models/project_services/jira_service.rb
@@ -18,7 +18,7 @@ class JiraService < IssueTrackerService
   end
 
   # {PROJECT-KEY}-{NUMBER} Examples: JIRA-1, PROJECT-1
-  def self.reference_pattern
+  def self.reference_pattern(only_long: true)
     @reference_pattern ||= %r{(?<issue>\b([A-Z][A-Z0-9_]+-)\d+)}
   end
 
diff --git a/app/services/issues/close_service.rb b/app/services/issues/close_service.rb
index ddef5281498..74459c3342c 100644
--- a/app/services/issues/close_service.rb
+++ b/app/services/issues/close_service.rb
@@ -16,13 +16,13 @@ module Issues
     # The code calling this method is responsible for ensuring that a user is
     # allowed to close the given issue.
     def close_issue(issue, commit: nil, notifications: true, system_note: true)
-      if project.jira_tracker? && project.jira_service.active
+      if project.jira_tracker? && project.jira_service.active && issue.is_a?(ExternalIssue)
         project.jira_service.close_issue(commit, issue)
         todo_service.close_issue(issue, current_user)
         return issue
       end
 
-      if project.default_issues_tracker? && issue.close
+      if project.issues_enabled? && issue.close
         event_service.close_issue(issue, current_user)
         create_note(issue, commit) if system_note
         notification_service.close_issue(issue, current_user) if notifications
diff --git a/app/views/layouts/nav/_new_project_sidebar.html.haml b/app/views/layouts/nav/_new_project_sidebar.html.haml
index 21f175291fa..00395b222e4 100644
--- a/app/views/layouts/nav/_new_project_sidebar.html.haml
+++ b/app/views/layouts/nav/_new_project_sidebar.html.haml
@@ -75,10 +75,10 @@
             Registry
 
     - if project_nav_tab? :issues
-      = nav_link(controller: @project.default_issues_tracker? ? [:issues, :labels, :milestones, :boards] : :issues) do
+      = nav_link(controller: @project.issues_enabled? ? [:issues, :labels, :milestones, :boards] : :issues) do
         = link_to project_issues_path(@project), title: 'Issues', class: 'shortcuts-issues' do
           %span
-            - if @project.default_issues_tracker?
+            - if @project.issues_enabled?
               %span.badge.count.issue_counter= number_with_delimiter(IssuesFinder.new(current_user, project_id: @project.id).execute.opened.count)
             Issues
 
@@ -113,7 +113,7 @@
                   Milestones
 
     - if project_nav_tab? :merge_requests
-      = nav_link(controller: @project.default_issues_tracker? ? :merge_requests : [:merge_requests, :labels, :milestones]) do
+      = nav_link(controller: @project.issues_enabled? ? :merge_requests : [:merge_requests, :labels, :milestones]) do
         = link_to project_merge_requests_path(@project), title: 'Merge Requests', class: 'shortcuts-merge_requests' do
           %span
             %span.badge.count.merge_counter.js-merge-counter= number_with_delimiter(MergeRequestsFinder.new(current_user, project_id: @project.id).execute.opened.count)
diff --git a/app/views/layouts/nav/_project.html.haml b/app/views/layouts/nav/_project.html.haml
index fb90bb4b472..924cd2e9681 100644
--- a/app/views/layouts/nav/_project.html.haml
+++ b/app/views/layouts/nav/_project.html.haml
@@ -23,16 +23,16 @@
             Registry
 
     - if project_nav_tab? :issues
-      = nav_link(controller: @project.default_issues_tracker? ? [:issues, :labels, :milestones, :boards] : :issues) do
+      = nav_link(controller: @project.issues_enabled? ? [:issues, :labels, :milestones, :boards] : :issues) do
         = link_to project_issues_path(@project), title: 'Issues', class: 'shortcuts-issues' do
           %span
             Issues
-            - if @project.default_issues_tracker?
+            - if @project.issues_enabled?
               %span.badge.count.issue_counter= number_with_delimiter(issuables_count_for_state(:issues, :opened, finder: IssuesFinder.new(current_user, project_id: @project.id)))
 
     - if project_nav_tab? :merge_requests
       - controllers = [:merge_requests, 'projects/merge_requests/conflicts']
-      - controllers.push(:merge_requests, :labels, :milestones) unless @project.default_issues_tracker?
+      - controllers.push(:merge_requests, :labels, :milestones) unless @project.issues_enabled?
       = nav_link(controller: controllers) do
         = link_to project_merge_requests_path(@project), title: 'Merge Requests', class: 'shortcuts-merge_requests' do
           %span
diff --git a/app/views/projects/merge_requests/index.html.haml b/app/views/projects/merge_requests/index.html.haml
index bfeb746ee83..c020e7db380 100644
--- a/app/views/projects/merge_requests/index.html.haml
+++ b/app/views/projects/merge_requests/index.html.haml
@@ -4,7 +4,7 @@
 - new_merge_request_path = project_new_merge_request_path(merge_project) if merge_project
 
 - page_title "Merge Requests"
-- unless @project.default_issues_tracker?
+- unless @project.issues_enabled?
   = content_for :sub_nav do
     = render "projects/merge_requests/head"
 
diff --git a/app/views/shared/_mr_head.html.haml b/app/views/shared/_mr_head.html.haml
index 4211ec6351d..e7355ae2eea 100644
--- a/app/views/shared/_mr_head.html.haml
+++ b/app/views/shared/_mr_head.html.haml
@@ -1,4 +1,4 @@
-- if @project.default_issues_tracker?
+- if @project.issues_enabled?
   = render "projects/issues/head"
 - else
   = render "projects/merge_requests/head"
diff --git a/lib/api/entities.rb b/lib/api/entities.rb
index 09a88869063..1719e9f7205 100644
--- a/lib/api/entities.rb
+++ b/lib/api/entities.rb
@@ -109,7 +109,7 @@ module API
         user.avatar_url(only_path: false)
       end
       expose :star_count, :forks_count
-      expose :open_issues_count, if: lambda { |project, options| project.feature_available?(:issues, options[:current_user]) && project.default_issues_tracker? }
+      expose :open_issues_count, if: lambda { |project, options| project.feature_available?(:issues, options[:current_user]) }
       expose :runners_token, if: lambda { |_project, options| options[:user_can_admin_project] }
       expose :public_builds, as: :public_jobs
       expose :ci_config_path
diff --git a/lib/api/merge_requests.rb b/lib/api/merge_requests.rb
index 6e2e13e0a24..f64ac659413 100644
--- a/lib/api/merge_requests.rb
+++ b/lib/api/merge_requests.rb
@@ -29,14 +29,6 @@ module API
           render_api_error!(errors, 400)
         end
 
-        def issue_entity(project)
-          if project.has_external_issue_tracker?
-            Entities::ExternalIssue
-          else
-            Entities::IssueBasic
-          end
-        end
-
         def find_merge_requests(args = {})
           args = params.merge(args)
 
@@ -278,7 +270,14 @@ module API
       get ':id/merge_requests/:merge_request_iid/closes_issues' do
         merge_request = find_merge_request_with_access(params[:merge_request_iid])
         issues = ::Kaminari.paginate_array(merge_request.closes_issues(current_user))
-        present paginate(issues), with: issue_entity(user_project), current_user: current_user
+        issues = paginate(issues)
+
+        external_issues, internal_issues = issues.partition { |issue| issue.is_a?(ExternalIssue) }
+
+        data = Entities::IssueBasic.represent(internal_issues, current_user: current_user)
+        data += Entities::ExternalIssue.represent(external_issues, current_user: current_user)
+
+        data.as_json
       end
     end
   end
diff --git a/lib/banzai/filter/issue_reference_filter.rb b/lib/banzai/filter/issue_reference_filter.rb
index ba1a5ac84b3..ce1ab977d3b 100644
--- a/lib/banzai/filter/issue_reference_filter.rb
+++ b/lib/banzai/filter/issue_reference_filter.rb
@@ -20,7 +20,7 @@ module Banzai
       end
 
       def url_for_object(issue, project)
-        IssuesHelper.url_for_issue(issue.iid, project, only_path: context[:only_path])
+        IssuesHelper.url_for_issue(issue.iid, project, only_path: context[:only_path], internal: true)
       end
 
       def project_from_ref(ref)
diff --git a/lib/banzai/reference_parser/external_issue_parser.rb b/lib/banzai/reference_parser/external_issue_parser.rb
index 6307c1b571a..1802cd04854 100644
--- a/lib/banzai/reference_parser/external_issue_parser.rb
+++ b/lib/banzai/reference_parser/external_issue_parser.rb
@@ -21,10 +21,14 @@ module Banzai
         gather_attributes_per_project(nodes, self.class.data_attribute)
       end
 
-      private
-
+      # we extract only external issue trackers references here, we don't extract cross-project references,
+      # so we don't need to do anything here.
       def can_read_reference?(user, ref_project, node)
-        can?(user, :read_issue, ref_project)
+        true
+      end
+
+      def nodes_visible_to_user(user, nodes)
+        nodes
       end
     end
   end
diff --git a/lib/gitlab/reference_extractor.rb b/lib/gitlab/reference_extractor.rb
index 7668ecacc4b..f5b757ace77 100644
--- a/lib/gitlab/reference_extractor.rb
+++ b/lib/gitlab/reference_extractor.rb
@@ -33,7 +33,12 @@ module Gitlab
 
     def issues
       if project && project.jira_tracker?
-        @references[:external_issue] ||= references(:external_issue)
+        if project.issues_enabled?
+          @references[:all_issues] ||= references(:external_issue) + references(:issue)
+        else
+          @references[:external_issue] ||= references(:external_issue) +
+            references(:issue).select { |i| i.project_id != project.id }
+        end
       else
         @references[:issue] ||= references(:issue)
       end
diff --git a/lib/gitlab/slash_commands/issue_command.rb b/lib/gitlab/slash_commands/issue_command.rb
index 87ea19b8806..3d96982b820 100644
--- a/lib/gitlab/slash_commands/issue_command.rb
+++ b/lib/gitlab/slash_commands/issue_command.rb
@@ -2,7 +2,7 @@ module Gitlab
   module SlashCommands
     class IssueCommand < BaseCommand
       def self.available?(project)
-        project.issues_enabled? && project.default_issues_tracker?
+        project.issues_enabled?
       end
 
       def collection
diff --git a/spec/features/issuables/markdown_references_spec.rb b/spec/features/issuables/markdown_references_spec.rb
new file mode 100644
index 00000000000..f51b2e4001a
--- /dev/null
+++ b/spec/features/issuables/markdown_references_spec.rb
@@ -0,0 +1,193 @@
+require 'rails_helper'
+
+describe 'Markdown References', :feature, :js do
+  let(:user)    { create(:user) }
+  let(:actual_project) { create(:project, :public) }
+  let(:merge_request) { create(:merge_request, target_project: actual_project, source_project: actual_project)}
+  let(:issue_actual_project) { create(:issue, project: actual_project) }
+  let!(:other_project) { create(:empty_project, :public) }
+  let!(:issue_other_project)   { create(:issue, project: other_project) }
+  let(:issues) { [issue_actual_project, issue_other_project] }
+
+  def build_note
+    markdown = "Referencing internal issue #{issue_actual_project.to_reference}, " +
+      "cross-project #{issue_other_project.to_reference(actual_project)} external JIRA-5 " +
+      "and non existing #999"
+
+    page.within('#diff-notes-app') do
+      fill_in 'note_note', with: markdown
+    end
+  end
+
+  shared_examples 'correct references' do
+    before do
+      remotelink = double(:remotelink, all: [], build: double(save!: true))
+
+      stub_request(:get, "https://jira.example.com/rest/api/2/issue/JIRA-5")
+      stub_request(:post, "https://jira.example.com/rest/api/2/issue/JIRA-5/comment")
+      allow_any_instance_of(JIRA::Resource::Issue).to receive(:remotelink).and_return(remotelink)
+
+      sign_in(user)
+      visit merge_request_path(merge_request)
+      build_note
+    end
+
+    def links_expectations
+      issues.each do |issue|
+        if referenced_issues.include?(issue)
+          expect(page).to have_link(issue.to_reference, href: issue_path(issue))
+        else
+          expect(page).not_to have_link(issue.to_reference, href: issue_path(issue))
+        end
+      end
+
+      if jira_referenced
+        expect(page).to have_link('JIRA-5', href: 'https://jira.example.com/browse/JIRA-5')
+      else
+        expect(page).not_to have_link('JIRA-5', href: 'https://jira.example.com/browse/JIRA-5')
+      end
+
+      expect(page).not_to have_link('#999')
+    end
+
+    it 'creates a link to the referenced issue on the preview' do
+      find('.js-md-preview-button').click
+      wait_for_requests
+
+      page.within('.md-preview-holder') do
+        links_expectations
+      end
+    end
+
+    it 'creates a link to the referenced issue after submit' do
+      click_button 'Comment'
+      wait_for_requests
+
+      page.within('#diff-notes-app') do
+        links_expectations
+      end
+    end
+
+    it 'creates a note on the referenced issues' do
+      click_button 'Comment'
+      wait_for_requests
+
+      if referenced_issues.include?(issue_actual_project)
+        visit issue_path(issue_actual_project)
+
+        page.within('#notes') do
+          expect(page).to have_content(
+            "#{user.to_reference} mentioned in merge request #{merge_request.to_reference}"
+          )
+        end
+      end
+
+      if referenced_issues.include?(issue_other_project)
+        visit issue_path(issue_other_project)
+
+        page.within('#notes') do
+          expect(page).to have_content(
+            "#{user.to_reference} mentioned in merge request #{merge_request.to_reference(other_project)}"
+          )
+        end
+      end
+    end
+  end
+
+  context 'when internal issues tracker is enabled for the other project' do
+    context 'when only internal issues tracker is enabled for the actual project' do
+      include_examples 'correct references' do
+        let(:referenced_issues) { [issue_actual_project, issue_other_project] }
+        let(:jira_referenced)   { false }
+      end
+    end
+
+    context 'when both external and internal issues trackers are enabled for the actual project' do
+      before do
+        create(:jira_service, project: actual_project)
+      end
+
+      include_examples 'correct references' do
+        let(:referenced_issues) { [issue_actual_project, issue_other_project] }
+        let(:jira_referenced)   { true }
+      end
+    end
+
+    context 'when only external issues tracker is enabled for the actual project' do
+      before do
+        create(:jira_service, project: actual_project)
+
+        actual_project.issues_enabled = false
+        actual_project.save!
+      end
+
+      include_examples 'correct references' do
+        let(:referenced_issues) { [issue_other_project] }
+        let(:jira_referenced)   { true }
+      end
+    end
+
+    context 'when no tracker is enabled for the actual project' do
+      before do
+        actual_project.issues_enabled = false
+        actual_project.save!
+      end
+
+      include_examples 'correct references' do
+        let(:referenced_issues) { [issue_other_project] }
+        let(:jira_referenced)   { false }
+      end
+    end
+  end
+
+  context 'when internal issues tracker is disabled for the other project' do
+    before do
+      other_project.issues_enabled = false
+      other_project.save!
+    end
+
+    context 'when only internal issues tracker is enabled for the actual project' do
+      include_examples 'correct references' do
+        let(:referenced_issues) { [issue_actual_project] }
+        let(:jira_referenced)   { false }
+      end
+    end
+
+    context 'when both external and internal issues trackers are enabled for the actual project' do
+      before do
+        create(:jira_service, project: actual_project)
+      end
+
+      include_examples 'correct references' do
+        let(:referenced_issues) { [issue_actual_project] }
+        let(:jira_referenced)   { true }
+      end
+    end
+
+    context 'when only external issues tracker is enabled for the actual project' do
+      before do
+        create(:jira_service, project: actual_project)
+
+        actual_project.issues_enabled = false
+        actual_project.save!
+      end
+
+      include_examples 'correct references' do
+        let(:referenced_issues) { [] }
+        let(:jira_referenced)   { true }
+      end
+    end
+
+    context 'when no issues tracker is enabled for the actual project' do
+      before do
+        actual_project.issues_enabled = false
+        actual_project.save!
+      end
+
+      include_examples 'correct references' do
+        let(:referenced_issues) { [] }
+        let(:jira_referenced)   { false }
+      end
+    end
+  end
+end
diff --git a/spec/features/projects/features_visibility_spec.rb b/spec/features/projects/features_visibility_spec.rb
index 2091c7b79d3..1588f8a828a 100644
--- a/spec/features/projects/features_visibility_spec.rb
+++ b/spec/features/projects/features_visibility_spec.rb
@@ -55,7 +55,7 @@ describe 'Edit Project Settings', feature: true do
         project.save!
         allow_any_instance_of(Project).to receive(:external_issue_tracker).and_return(JiraService.new)
 
-        visit namespace_project_path(project.namespace, project)
+        visit project_path(project)
 
         expect(page).not_to have_selector('.shortcuts-issues')
       end
diff --git a/spec/helpers/issues_helper_spec.rb b/spec/helpers/issues_helper_spec.rb
index 8f7f17a484f..9524a101e74 100644
--- a/spec/helpers/issues_helper_spec.rb
+++ b/spec/helpers/issues_helper_spec.rb
@@ -8,7 +8,7 @@ describe IssuesHelper do
   describe "url_for_issue" do
     let(:issues_url) { ext_project.external_issue_tracker.issues_url}
     let(:ext_expected) { issues_url.gsub(':id', issue.iid.to_s).gsub(':project_id', ext_project.id.to_s) }
-    let(:int_expected) { polymorphic_path([@project.namespace, project, issue]) }
+    let(:int_expected) { polymorphic_path([@project.namespace, @project, issue]) }
 
     it "returns internal path if used internal tracker" do
       @project = project
@@ -22,6 +22,12 @@ describe IssuesHelper do
       expect(url_for_issue(issue.iid)).to match(ext_expected)
     end
 
+    it "returns path to internal issue when internal option passed" do
+      @project = ext_project
+
+      expect(url_for_issue(issue.iid, ext_project, internal: true)).to match(int_expected)
+    end
+
     it "returns empty string if project nil" do
       @project = nil
 
diff --git a/spec/lib/banzai/filter/external_issue_reference_filter_spec.rb b/spec/lib/banzai/filter/external_issue_reference_filter_spec.rb
index b7d82c36ddd..fb320e0148a 100644
--- a/spec/lib/banzai/filter/external_issue_reference_filter_spec.rb
+++ b/spec/lib/banzai/filter/external_issue_reference_filter_spec.rb
@@ -108,6 +108,11 @@ describe Banzai::Filter::ExternalIssueReferenceFilter, lib: true do
     let(:issue) { ExternalIssue.new("#123", project) }
     let(:reference) { issue.to_reference }
 
+    before do
+      project.issues_enabled = false
+      project.save!
+    end
+
     it_behaves_like "external issue tracker"
   end
 
diff --git a/spec/lib/banzai/pipeline/gfm_pipeline_spec.rb b/spec/lib/banzai/pipeline/gfm_pipeline_spec.rb
index 1eb90dc1847..601ffbb5456 100644
--- a/spec/lib/banzai/pipeline/gfm_pipeline_spec.rb
+++ b/spec/lib/banzai/pipeline/gfm_pipeline_spec.rb
@@ -4,26 +4,87 @@ describe Banzai::Pipeline::GfmPipeline do
   describe 'integration between parsing regular and external issue references' do
     let(:project) { create(:redmine_project, :public) }
 
-    it 'allows to use shorthand external reference syntax for Redmine' do
-      markdown = '#12'
+    context 'when internal issue tracker is enabled' do
+      context 'when shorthand pattern #ISSUE_ID is used' do
+        it 'links an internal issue  if it exists' do
+          issue = create(:issue, project: project)
+          markdown = issue.to_reference(project, full: true)
 
-      result = described_class.call(markdown, project: project)[:output]
-      link = result.css('a').first
+          result = described_class.call(markdown, project: project)[:output]
+          link = result.css('a').first
 
-      expect(link['href']).to eq 'http://redmine/projects/project_name_in_redmine/issues/12'
+          expect(link['href']).to eq(
+            Gitlab::Routing.url_helpers.project_issue_path(project, issue)
+          )
+        end
+
+        it 'does not link any issue if it does not exist on GitLab' do
+          markdown = '#12'
+
+          result = described_class.call(markdown, project: project)[:output]
+          expect(result.css('a')).to be_empty
+        end
+      end
+
+      it 'allows to use long external reference syntax for Redmine' do
+        markdown = 'API_32-12'
+
+        result = described_class.call(markdown, project: project)[:output]
+        link = result.css('a').first
+
+        expect(link['href']).to eq 'http://redmine/projects/project_name_in_redmine/issues/12'
+      end
+
+      it 'parses cross-project references to regular issues' do
+        other_project = create(:empty_project, :public)
+        issue = create(:issue, project: other_project)
+        markdown = issue.to_reference(project, full: true)
+
+        result = described_class.call(markdown, project: project)[:output]
+        link = result.css('a').first
+
+        expect(link['href']).to eq(
+          Gitlab::Routing.url_helpers.project_issue_path(other_project, issue)
+        )
+      end
     end
 
-    it 'parses cross-project references to regular issues' do
-      other_project = create(:empty_project, :public)
-      issue = create(:issue, project: other_project)
-      markdown = issue.to_reference(project, full: true)
+    context 'when internal issue tracker is disabled' do
+      before do
+        project.issues_enabled = false
+        project.save!
+      end
+
+      it 'allows to use shorthand external reference syntax for Redmine' do
+        markdown = '#12'
+
+        result = described_class.call(markdown, project: project)[:output]
+        link = result.css('a').first
+
+        expect(link['href']).to eq 'http://redmine/projects/project_name_in_redmine/issues/12'
+      end
+
+      it 'allows to use long external reference syntax for Redmine' do
+        markdown = 'API_32-12'
+
+        result = described_class.call(markdown, project: project)[:output]
+        link = result.css('a').first
+
+        expect(link['href']).to eq 'http://redmine/projects/project_name_in_redmine/issues/12'
+      end
+
+      it 'parses cross-project references to regular issues' do
+        other_project = create(:empty_project, :public)
+        issue = create(:issue, project: other_project)
+        markdown = issue.to_reference(project, full: true)
 
-      result = described_class.call(markdown, project: project)[:output]
-      link = result.css('a').first
+        result = described_class.call(markdown, project: project)[:output]
+        link = result.css('a').first
 
-      expect(link['href']).to eq(
-        Gitlab::Routing.url_helpers.project_issue_path(other_project, issue)
-      )
+        expect(link['href']).to eq(
+          Gitlab::Routing.url_helpers.project_issue_path(other_project, issue)
+        )
+      end
     end
   end
 end
diff --git a/spec/lib/gitlab/reference_extractor_spec.rb b/spec/lib/gitlab/reference_extractor_spec.rb
index 84cfd934fa0..917692e9c6c 100644
--- a/spec/lib/gitlab/reference_extractor_spec.rb
+++ b/spec/lib/gitlab/reference_extractor_spec.rb
@@ -183,11 +183,34 @@ describe Gitlab::ReferenceExtractor, lib: true do
 
   context 'with an external issue tracker' do
     let(:project) { create(:jira_project) }
+    let(:issue)   { create(:issue, project: project) }
+
+    context 'when GitLab issues are enabled' do
+      it 'returns both JIRA and internal issues' do
+        subject.analyze("JIRA-123 and FOOBAR-4567 and #{issue.to_reference}")
+        expect(subject.issues).to eq [ExternalIssue.new('JIRA-123', project),
+                                      ExternalIssue.new('FOOBAR-4567', project),
+                                      issue]
+      end
+
+      it 'returns only JIRA issues if the internal one does not exists' do
+        subject.analyze("JIRA-123 and FOOBAR-4567 and #999")
+        expect(subject.issues).to eq [ExternalIssue.new('JIRA-123', project),
+                                      ExternalIssue.new('FOOBAR-4567', project)]
+      end
+    end
 
-    it 'returns JIRA issues for a JIRA-integrated project' do
-      subject.analyze('JIRA-123 and FOOBAR-4567')
-      expect(subject.issues).to eq [ExternalIssue.new('JIRA-123', project),
-                                    ExternalIssue.new('FOOBAR-4567', project)]
+    context 'when GitLab issues are disabled' do
+      before do
+        project.issues_enabled = false
+        project.save!
+      end
+
+      it 'returns only JIRA issues' do
+        subject.analyze("JIRA-123 and FOOBAR-4567 and #{issue.to_reference}")
+        expect(subject.issues).to eq [ExternalIssue.new('JIRA-123', project),
+                                      ExternalIssue.new('FOOBAR-4567', project)]
+      end
     end
   end
 
diff --git a/spec/models/concerns/mentionable_spec.rb b/spec/models/concerns/mentionable_spec.rb
index e2a29e0ae70..1ad811736af 100644
--- a/spec/models/concerns/mentionable_spec.rb
+++ b/spec/models/concerns/mentionable_spec.rb
@@ -174,25 +174,25 @@ describe Commit, 'Mentionable' do
     it "is false when message doesn't reference anything" do
       allow(commit.raw).to receive(:message).and_return "WIP: Do something"
 
-      expect(commit.matches_cross_reference_regex?).to be false
+      expect(commit.matches_cross_reference_regex?).to be_falsey
     end
 
     it 'is true if issue #number mentioned in title' do
       allow(commit.raw).to receive(:message).and_return "#1"
 
-      expect(commit.matches_cross_reference_regex?).to be true
+      expect(commit.matches_cross_reference_regex?).to be_truthy
     end
 
     it 'is true if references an MR' do
       allow(commit.raw).to receive(:message).and_return "See merge request !12"
 
-      expect(commit.matches_cross_reference_regex?).to be true
+      expect(commit.matches_cross_reference_regex?).to be_truthy
     end
 
     it 'is true if references a commit' do
       allow(commit.raw).to receive(:message).and_return "a1b2c3d4"
 
-      expect(commit.matches_cross_reference_regex?).to be true
+      expect(commit.matches_cross_reference_regex?).to be_truthy
     end
 
     it 'is true if issue referenced by url' do
@@ -200,7 +200,7 @@ describe Commit, 'Mentionable' do
 
       allow(commit.raw).to receive(:message).and_return Gitlab::UrlBuilder.build(issue)
 
-      expect(commit.matches_cross_reference_regex?).to be true
+      expect(commit.matches_cross_reference_regex?).to be_truthy
     end
 
     context 'with external issue tracker' do
@@ -209,7 +209,13 @@ describe Commit, 'Mentionable' do
       it 'is true if external issues referenced' do
         allow(commit.raw).to receive(:message).and_return 'JIRA-123'
 
-        expect(commit.matches_cross_reference_regex?).to be true
+        expect(commit.matches_cross_reference_regex?).to be_truthy
+      end
+
+      it 'is true if internal issues referenced' do
+        allow(commit.raw).to receive(:message).and_return '#123'
+
+        expect(commit.matches_cross_reference_regex?).to be_truthy
       end
     end
   end
diff --git a/spec/models/merge_request_spec.rb b/spec/models/merge_request_spec.rb
index 1eadc28869f..6f6a8ac91b8 100644
--- a/spec/models/merge_request_spec.rb
+++ b/spec/models/merge_request_spec.rb
@@ -155,13 +155,53 @@ describe MergeRequest, models: true do
       expect { subject.cache_merge_request_closes_issues!(subject.author) }.to change(subject.merge_requests_closing_issues, :count).by(1)
     end
 
-    it 'does not cache issues from external trackers' do
-      subject.project.update_attribute(:has_external_issue_tracker, true)
-      issue  = ExternalIssue.new('JIRA-123', subject.project)
-      commit = double('commit1', safe_message: "Fixes #{issue.to_reference}")
-      allow(subject).to receive(:commits).and_return([commit])
+    context 'when both internal and external issue trackers are enabled' do
+      before do
+        subject.project.has_external_issue_tracker = true
+        subject.project.save!
+      end
+
+      it 'does not cache issues from external trackers' do
+        issue  = ExternalIssue.new('JIRA-123', subject.project)
+        commit = double('commit1', safe_message: "Fixes #{issue.to_reference}")
+        allow(subject).to receive(:commits).and_return([commit])
 
-      expect { subject.cache_merge_request_closes_issues!(subject.author) }.not_to change(subject.merge_requests_closing_issues, :count)
+        expect { subject.cache_merge_request_closes_issues!(subject.author) }.not_to change(subject.merge_requests_closing_issues, :count)
+      end
+
+      it 'caches an internal issue' do
+        issue  = create(:issue, project: subject.project)
+        commit = double('commit1', safe_message: "Fixes #{issue.to_reference}")
+        allow(subject).to receive(:commits).and_return([commit])
+
+        expect { subject.cache_merge_request_closes_issues!(subject.author) }
+          .to change(subject.merge_requests_closing_issues, :count).by(1)
+      end
+    end
+
+    context 'when only external issue tracker enabled' do
+      before do
+        subject.project.has_external_issue_tracker = true
+        subject.project.issues_enabled = false
+        subject.project.save!
+      end
+
+      it 'does not cache issues from external trackers' do
+        issue  = ExternalIssue.new('JIRA-123', subject.project)
+        commit = double('commit1', safe_message: "Fixes #{issue.to_reference}")
+        allow(subject).to receive(:commits).and_return([commit])
+
+        expect { subject.cache_merge_request_closes_issues!(subject.author) }.not_to change(subject.merge_requests_closing_issues, :count)
+      end
+
+      it 'does not cache an internal issue' do
+        issue  = create(:issue, project: subject.project)
+        commit = double('commit1', safe_message: "Fixes #{issue.to_reference}")
+        allow(subject).to receive(:commits).and_return([commit])
+
+        expect { subject.cache_merge_request_closes_issues!(subject.author) }
+          .not_to change(subject.merge_requests_closing_issues, :count)
+      end
     end
   end
 
diff --git a/spec/models/project_spec.rb b/spec/models/project_spec.rb
index fdcb011d685..8d916b79b13 100644
--- a/spec/models/project_spec.rb
+++ b/spec/models/project_spec.rb
@@ -533,15 +533,48 @@ describe Project, models: true do
     end
 
     context 'with external issues tracker' do
+      let!(:internal_issue) { create(:issue, project: project) }
       before do
-        allow(project).to receive(:default_issues_tracker?).and_return(false)
+        allow(project).to receive(:external_issue_tracker).and_return(true)
       end
 
-      it 'returns an ExternalIssue' do
-        issue = project.get_issue('FOO-1234', user)
-        expect(issue).to be_kind_of(ExternalIssue)
-        expect(issue.iid).to eq 'FOO-1234'
-        expect(issue.project).to eq project
+      context 'when internal issues are enabled' do
+        it 'returns interlan issue' do
+          issue = project.get_issue(internal_issue.iid, user)
+
+          expect(issue).to be_kind_of(Issue)
+          expect(issue.iid).to eq(internal_issue.iid)
+          expect(issue.project).to eq(project)
+        end
+
+        it 'returns an ExternalIssue when internal issue does not exists' do
+          issue = project.get_issue('FOO-1234', user)
+
+          expect(issue).to be_kind_of(ExternalIssue)
+          expect(issue.iid).to eq('FOO-1234')
+          expect(issue.project).to eq(project)
+        end
+      end
+
+      context 'when internal issues are disabled' do
+        before do
+          project.issues_enabled = false
+          project.save!
+        end
+
+        it 'returns always an External issues' do
+          issue = project.get_issue(internal_issue.iid, user)
+          expect(issue).to be_kind_of(ExternalIssue)
+          expect(issue.iid).to eq(internal_issue.iid.to_s)
+          expect(issue.project).to eq(project)
+        end
+
+        it 'returns an ExternalIssue when internal issue does not exists' do
+          issue = project.get_issue('FOO-1234', user)
+          expect(issue).to be_kind_of(ExternalIssue)
+          expect(issue.iid).to eq('FOO-1234')
+          expect(issue.project).to eq(project)
+        end
       end
     end
   end
diff --git a/spec/requests/api/merge_requests_spec.rb b/spec/requests/api/merge_requests_spec.rb
index 9098ae6bcda..35b6522ea98 100644
--- a/spec/requests/api/merge_requests_spec.rb
+++ b/spec/requests/api/merge_requests_spec.rb
@@ -794,18 +794,24 @@ describe API::MergeRequests do
 
     it 'handles external issues' do
       jira_project = create(:jira_project, :public, name: 'JIR_EXT1')
-      issue = ExternalIssue.new("#{jira_project.name}-123", jira_project)
-      merge_request = create(:merge_request, :simple, author: user, assignee: user, source_project: jira_project)
-      merge_request.update_attribute(:description, "Closes #{issue.to_reference(jira_project)}")
+      ext_issue = ExternalIssue.new("#{jira_project.name}-123", jira_project)
+      issue = create(:issue, project: jira_project)
+      description = "Closes #{ext_issue.to_reference(jira_project)}\ncloses #{issue.to_reference}"
+      merge_request = create(:merge_request,
+        :simple, author: user, assignee: user, source_project: jira_project, description: description)
 
       get api("/projects/#{jira_project.id}/merge_requests/#{merge_request.iid}/closes_issues", user)
 
       expect(response).to have_http_status(200)
       expect(response).to include_pagination_headers
       expect(json_response).to be_an Array
-      expect(json_response.length).to eq(1)
+      expect(json_response.length).to eq(2)
+      expect(json_response.second['title']).to eq(ext_issue.title)
+      expect(json_response.second['id']).to eq(ext_issue.id)
+      expect(json_response.second['confidential']).to be_nil
       expect(json_response.first['title']).to eq(issue.title)
       expect(json_response.first['id']).to eq(issue.id)
+      expect(json_response.first['confidential']).not_to be_nil
     end
 
     it 'returns 403 if the user has no access to the merge request' do
diff --git a/spec/requests/api/projects_spec.rb b/spec/requests/api/projects_spec.rb
index 6dbde8bad31..457f64cc88c 100644
--- a/spec/requests/api/projects_spec.rb
+++ b/spec/requests/api/projects_spec.rb
@@ -159,6 +159,31 @@ describe API::Projects do
         expect(json_response.first).to include 'statistics'
       end
 
+      context 'when external issue tracker is enabled' do
+        let!(:jira_service) { create(:jira_service, project: project) }
+
+        it 'includes open_issues_count' do
+          get api('/projects', user)
+
+          expect(response.status).to eq 200
+          expect(response).to include_pagination_headers
+          expect(json_response).to be_an Array
+          expect(json_response.first.keys).to include('open_issues_count')
+          expect(json_response.find { |hash| hash['id'] == project.id }.keys).to include('open_issues_count')
+        end
+
+        it 'does not include open_issues_count if issues are disabled' do
+          project.project_feature.update_attribute(:issues_access_level, ProjectFeature::DISABLED)
+
+          get api('/projects', user)
+
+          expect(response.status).to eq 200
+          expect(response).to include_pagination_headers
+          expect(json_response).to be_an Array
+          expect(json_response.find { |hash| hash['id'] == project.id }.keys).not_to include('open_issues_count')
+        end
+      end
+
       context 'and with simple=true' do
         it 'returns a simplified version of all the projects' do
           expected_keys = %w(id http_url_to_repo web_url name name_with_namespace path path_with_namespace)
diff --git a/spec/services/git_push_service_spec.rb b/spec/services/git_push_service_spec.rb
index c493c08a7ae..f801506f1b6 100644
--- a/spec/services/git_push_service_spec.rb
+++ b/spec/services/git_push_service_spec.rb
@@ -488,21 +488,57 @@ describe GitPushService, services: true do
           end
         end
 
-        context "using wrong markdown" do
-          let(:message) { "this is some work.\n\ncloses #1" }
+        context "using internal issue reference" do
+          context 'when internal issues are disabled' do
+            before do
+              project.issues_enabled = false
+              project.save!
+            end
+            let(:message) { "this is some work.\n\ncloses #1" }
+
+            it "does not initiates one api call to jira server to close the issue" do
+              execute_service(project, commit_author, @oldrev, @newrev, @ref )
+
+              expect(WebMock).not_to have_requested(:post, jira_api_transition_url('JIRA-1'))
+            end
+
+            it "does not initiates one api call to jira server to comment on the issue" do
+              execute_service(project, commit_author, @oldrev, @newrev, @ref )
+
+              expect(WebMock).not_to have_requested(:post, jira_api_comment_url('JIRA-1')).with(
+                body: comment_body
+              ).once
+            end
+          end
 
-          it "does not initiates one api call to jira server to close the issue" do
-            execute_service(project, commit_author, @oldrev, @newrev, @ref )
+          context 'when internal issues are enabled' do
+            let(:issue) { create(:issue, project: project) }
+            let(:message) { "this is some work.\n\ncloses JIRA-1 \n\n closes #{issue.to_reference}" }
 
-            expect(WebMock).not_to have_requested(:post, jira_api_transition_url('JIRA-1'))
-          end
+            it "initiates one api call to jira server to close the jira issue" do
+              execute_service(project, commit_author, @oldrev, @newrev, @ref )
 
-          it "does not initiates one api call to jira server to comment on the issue" do
-            execute_service(project, commit_author, @oldrev, @newrev, @ref )
+              expect(WebMock).to have_requested(:post, jira_api_transition_url('JIRA-1')).once
+            end
 
-            expect(WebMock).not_to have_requested(:post, jira_api_comment_url('JIRA-1')).with(
-              body: comment_body
-            ).once
+            it "initiates one api call to jira server to comment on the jira issue" do
+              execute_service(project, commit_author, @oldrev, @newrev, @ref )
+
+              expect(WebMock).to have_requested(:post, jira_api_comment_url('JIRA-1')).with(
+                body: comment_body
+              ).once
+            end
+
+            it "closes the internal issue" do
+              execute_service(project, commit_author, @oldrev, @newrev, @ref )
+              expect(issue.reload).to be_closed
+            end
+
+            it "adds a note indicating that the issue is now closed" do
+              expect(SystemNoteService).to receive(:change_status)
+                .with(issue, project, commit_author, "closed", closing_commit)
+              execute_service(project, commit_author, @oldrev, @newrev, @ref )
+            end
           end
         end
       end
diff --git a/spec/services/issues/close_service_spec.rb b/spec/services/issues/close_service_spec.rb
index d6f4c694069..da8b60f1337 100644
--- a/spec/services/issues/close_service_spec.rb
+++ b/spec/services/issues/close_service_spec.rb
@@ -98,13 +98,13 @@ describe Issues::CloseService, services: true do
       end
     end
 
-    context 'external issue tracker' do
+    context 'internal issues disabled' do
       before do
-        allow(project).to receive(:default_issues_tracker?).and_return(false)
-        described_class.new(project, user).close_issue(issue)
+        project.issues_enabled = false
+        project.save!
       end
 
-      it 'closes the issue' do
+      it 'does not close the issue' do
         expect(issue).to be_valid
         expect(issue).to be_opened
         expect(todo.reload).to be_pending
diff --git a/spec/services/merge_requests/build_service_spec.rb b/spec/services/merge_requests/build_service_spec.rb
index 01ef52396d7..a40d4c877bc 100644
--- a/spec/services/merge_requests/build_service_spec.rb
+++ b/spec/services/merge_requests/build_service_spec.rb
@@ -207,7 +207,7 @@ describe MergeRequests::BuildService, services: true do
         let(:source_branch) { '12345-fix-issue' }
 
         before do
-          allow(project).to receive(:default_issues_tracker?).and_return(false)
+          allow(project).to receive(:external_issue_tracker).and_return(true)
         end
 
         it 'sets the title to: Resolves External Issue $issue-iid' do