Merge branch 'master' into zj-project-templates

* master: (623 commits)
  Fix issues with pdf-js dependencies
  fix missing changelog entries for security release on 2017-01-23
  Update top bar issues icon
  Fix pipeline icon in contextual nav for projects
  Since mysql is not a priority anymore, test it less
  Fix order of CI lint ace editor loading
  Add container registry and spam logs icons
  Fix different Markdown styles
  Backport to CE for:
  Make new dropdown dividers full width
  Fix spec
  Fix spec
  Fix spec
  Bump GITLAB_SHELL_VERSION and GITALY_VERSION to support unhiding refs
  Add changelog
  Install yarn via apt in update guides
  Use long curl options
  fix
  Add a spec for concurrent process
  Remove monkey-patched Array.prototype.first() and last() methods
  ...

17 files changed, 134 insertions, 125 deletions

diff --git a/app/controllers/admin/application_settings_controller.rb b/app/controllers/admin/application_settings_controller.rb
index c1bc4c0d675..8367c22d1ca 100644
--- a/app/controllers/admin/application_settings_controller.rb
+++ b/app/controllers/admin/application_settings_controller.rb
@@ -76,88 +76,13 @@ class Admin::ApplicationSettingsController < Admin::ApplicationController
     params.delete(:domain_blacklist_raw) if params[:domain_blacklist_file]
 
     params.require(:application_setting).permit(
-      application_setting_params_ce
+      visible_application_setting_attributes
     )
   end
 
-  def application_setting_params_ce
-    [
-      :admin_notification_email,
-      :after_sign_out_path,
-      :after_sign_up_text,
-      :akismet_api_key,
-      :akismet_enabled,
-      :container_registry_token_expire_delay,
-      :default_artifacts_expire_in,
-      :default_branch_protection,
-      :default_group_visibility,
-      :default_project_visibility,
-      :default_projects_limit,
-      :default_snippet_visibility,
-      :domain_blacklist_enabled,
+  def visible_application_setting_attributes
+    ApplicationSettingsHelper.visible_attributes + [
       :domain_blacklist_file,
-      :domain_blacklist_raw,
-      :domain_whitelist_raw,
-      :email_author_in_body,
-      :enabled_git_access_protocol,
-      :gravatar_enabled,
-      :help_page_text,
-      :help_page_hide_commercial_content,
-      :help_page_support_url,
-      :home_page_url,
-      :housekeeping_bitmaps_enabled,
-      :housekeeping_enabled,
-      :housekeeping_full_repack_period,
-      :housekeeping_gc_period,
-      :housekeeping_incremental_repack_period,
-      :html_emails_enabled,
-      :koding_enabled,
-      :koding_url,
-      :password_authentication_enabled,
-      :plantuml_enabled,
-      :plantuml_url,
-      :max_artifacts_size,
-      :max_attachment_size,
-      :max_pages_size,
-      :metrics_enabled,
-      :metrics_host,
-      :metrics_method_call_threshold,
-      :metrics_packet_size,
-      :metrics_pool_size,
-      :metrics_port,
-      :metrics_sample_interval,
-      :metrics_timeout,
-      :performance_bar_allowed_group_id,
-      :performance_bar_enabled,
-      :recaptcha_enabled,
-      :recaptcha_private_key,
-      :recaptcha_site_key,
-      :repository_checks_enabled,
-      :require_two_factor_authentication,
-      :session_expire_delay,
-      :sign_in_text,
-      :signup_enabled,
-      :sentry_dsn,
-      :sentry_enabled,
-      :clientside_sentry_dsn,
-      :clientside_sentry_enabled,
-      :send_user_confirmation_email,
-      :shared_runners_enabled,
-      :shared_runners_text,
-      :sidekiq_throttling_enabled,
-      :sidekiq_throttling_factor,
-      :two_factor_grace_period,
-      :user_default_external,
-      :user_oauth_applications,
-      :unique_ips_limit_per_user,
-      :unique_ips_limit_time_window,
-      :unique_ips_limit_enabled,
-      :version_check_enabled,
-      :terminal_max_session_time,
-      :polling_interval_multiplier,
-      :prometheus_metrics_enabled,
-      :usage_ping_enabled,
-
       disabled_oauth_sign_in_sources: [],
       import_sources: [],
       repository_storages: [],
diff --git a/app/controllers/admin/applications_controller.rb b/app/controllers/admin/applications_controller.rb
index 434ff6b2a62..16590e66d61 100644
--- a/app/controllers/admin/applications_controller.rb
+++ b/app/controllers/admin/applications_controller.rb
@@ -50,6 +50,6 @@ class Admin::ApplicationsController < Admin::ApplicationController
 
   # Only allow a trusted parameter "white list" through.
   def application_params
-    params[:doorkeeper_application].permit(:name, :redirect_uri, :scopes)
+    params.require(:doorkeeper_application).permit(:name, :redirect_uri, :trusted, :scopes)
   end
 end
diff --git a/app/controllers/admin/dashboard_controller.rb b/app/controllers/admin/dashboard_controller.rb
index 8360ce08bdc..05e749c00c0 100644
--- a/app/controllers/admin/dashboard_controller.rb
+++ b/app/controllers/admin/dashboard_controller.rb
@@ -1,6 +1,6 @@
 class Admin::DashboardController < Admin::ApplicationController
   def index
-    @projects = Project.with_route.limit(10)
+    @projects = Project.without_deleted.with_route.limit(10)
     @users = User.limit(10)
     @groups = Group.with_route.limit(10)
   end
diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
index 43462b13903..d14b1dbecf6 100644
--- a/app/controllers/application_controller.rb
+++ b/app/controllers/application_controller.rb
@@ -70,6 +70,16 @@ class ApplicationController < ActionController::Base
 
   protected
 
+  def append_info_to_payload(payload)
+    super
+    payload[:remote_ip] = request.remote_ip
+
+    if current_user.present?
+      payload[:user_id] = current_user.id
+      payload[:username] = current_user.username
+    end
+  end
+
   # This filter handles both private tokens and personal access tokens
   def authenticate_user_from_private_token!
     token = params[:private_token].presence || request.headers['PRIVATE-TOKEN'].presence
diff --git a/app/controllers/concerns/notes_actions.rb b/app/controllers/concerns/notes_actions.rb
index a57d9e6e6c0..af5f683bab5 100644
--- a/app/controllers/concerns/notes_actions.rb
+++ b/app/controllers/concerns/notes_actions.rb
@@ -4,6 +4,7 @@ module NotesActions
 
   included do
     before_action :authorize_admin_note!, only: [:update, :destroy]
+    before_action :note_project, only: [:create]
   end
 
   def index
@@ -28,7 +29,8 @@ module NotesActions
       merge_request_diff_head_sha: params[:merge_request_diff_head_sha],
       in_reply_to_discussion_id: params[:in_reply_to_discussion_id]
     )
-    @note = Notes::CreateService.new(project, current_user, create_params).execute
+
+    @note = Notes::CreateService.new(note_project, current_user, create_params).execute
 
     if @note.is_a?(Note)
       Banzai::NoteRenderer.render([@note], @project, current_user)
@@ -177,4 +179,22 @@ module NotesActions
   def notes_finder
     @notes_finder ||= NotesFinder.new(project, current_user, finder_params)
   end
+
+  def note_project
+    return @note_project if defined?(@note_project)
+    return nil unless project
+
+    note_project_id = params[:note_project_id]
+
+    @note_project =
+      if note_project_id.present?
+        Project.find(note_project_id)
+      else
+        project
+      end
+
+    return access_denied! unless can?(current_user, :create_note, @note_project)
+
+    @note_project
+  end
 end
diff --git a/app/controllers/dashboard/todos_controller.rb b/app/controllers/dashboard/todos_controller.rb
index 59e5b5e4775..a8b2b93b458 100644
--- a/app/controllers/dashboard/todos_controller.rb
+++ b/app/controllers/dashboard/todos_controller.rb
@@ -13,7 +13,7 @@ class Dashboard::TodosController < Dashboard::ApplicationController
   end
 
   def destroy
-    TodoService.new.mark_todos_as_done_by_ids([params[:id]], current_user)
+    TodoService.new.mark_todos_as_done_by_ids(params[:id], current_user)
 
     respond_to do |format|
       format.html do
@@ -37,7 +37,7 @@ class Dashboard::TodosController < Dashboard::ApplicationController
   end
 
   def restore
-    TodoService.new.mark_todos_as_pending_by_ids([params[:id]], current_user)
+    TodoService.new.mark_todos_as_pending_by_ids(params[:id], current_user)
 
     render json: todos_counts
   end
diff --git a/app/controllers/profiles/gpg_keys_controller.rb b/app/controllers/profiles/gpg_keys_controller.rb
new file mode 100644
index 00000000000..6779cc6ddac
--- /dev/null
+++ b/app/controllers/profiles/gpg_keys_controller.rb
@@ -0,0 +1,47 @@
+class Profiles::GpgKeysController < Profiles::ApplicationController
+  before_action :set_gpg_key, only: [:destroy, :revoke]
+
+  def index
+    @gpg_keys = current_user.gpg_keys
+    @gpg_key = GpgKey.new
+  end
+
+  def create
+    @gpg_key = current_user.gpg_keys.new(gpg_key_params)
+
+    if @gpg_key.save
+      redirect_to profile_gpg_keys_path
+    else
+      @gpg_keys = current_user.gpg_keys.select(&:persisted?)
+      render :index
+    end
+  end
+
+  def destroy
+    @gpg_key.destroy
+
+    respond_to do |format|
+      format.html { redirect_to profile_gpg_keys_url, status: 302 }
+      format.js { head :ok }
+    end
+  end
+
+  def revoke
+    @gpg_key.revoke
+
+    respond_to do |format|
+      format.html { redirect_to profile_gpg_keys_url, status: 302 }
+      format.js { head :ok }
+    end
+  end
+
+  private
+
+  def gpg_key_params
+    params.require(:gpg_key).permit(:key)
+  end
+
+  def set_gpg_key
+    @gpg_key = current_user.gpg_keys.find(params[:id])
+  end
+end
diff --git a/app/controllers/projects/application_controller.rb b/app/controllers/projects/application_controller.rb
index 95de3a44641..221e01b415a 100644
--- a/app/controllers/projects/application_controller.rb
+++ b/app/controllers/projects/application_controller.rb
@@ -22,6 +22,7 @@ class Projects::ApplicationController < ApplicationController
 
   def project
     return @project if @project
+    return nil unless params[:project_id] || params[:id]
 
     path = File.join(params[:namespace_id], params[:project_id] || params[:id])
     auth_proc = ->(project) { !project.pending_delete? }
diff --git a/app/controllers/projects/boards/issues_controller.rb b/app/controllers/projects/boards/issues_controller.rb
index da9b789d617..653e7bc7e40 100644
--- a/app/controllers/projects/boards/issues_controller.rb
+++ b/app/controllers/projects/boards/issues_controller.rb
@@ -66,7 +66,8 @@ module Projects
       end
 
       def filter_params
-        params.merge(board_id: params[:board_id], id: params[:list_id]).compact
+        params.merge(board_id: params[:board_id], id: params[:list_id])
+          .reject { |_, value| value.nil? }
       end
 
       def move_params
diff --git a/app/controllers/projects/branches_controller.rb b/app/controllers/projects/branches_controller.rb
index 86058531179..747768eefb1 100644
--- a/app/controllers/projects/branches_controller.rb
+++ b/app/controllers/projects/branches_controller.rb
@@ -8,7 +8,7 @@ class Projects::BranchesController < Projects::ApplicationController
   before_action :authorize_push_code!, only: [:new, :create, :destroy, :destroy_all_merged]
 
   def index
-    @sort = params[:sort].presence || sort_value_name
+    @sort = params[:sort].presence || sort_value_recently_updated
     @branches = BranchesFinder.new(@repository, params).execute
     @branches = Kaminari.paginate_array(@branches).page(params[:page])
 
diff --git a/app/controllers/projects/commits_controller.rb b/app/controllers/projects/commits_controller.rb
index 37b5a6e9d48..2de9900d449 100644
--- a/app/controllers/projects/commits_controller.rb
+++ b/app/controllers/projects/commits_controller.rb
@@ -6,18 +6,9 @@ class Projects::CommitsController < Projects::ApplicationController
   before_action :require_non_empty_project
   before_action :assign_ref_vars
   before_action :authorize_download_code!
+  before_action :set_commits
 
   def show
-    @limit, @offset = (params[:limit] || 40).to_i, (params[:offset] || 0).to_i
-    search = params[:search]
-
-    @commits =
-      if search.present?
-        @repository.find_commits_by_message(search, @ref, @path, @limit, @offset)
-      else
-        @repository.commits(@ref, path: @path, limit: @limit, offset: @offset)
-      end
-
     @note_counts = project.notes.where(commit_id: @commits.map(&:id))
       .group(:commit_id).count
 
@@ -37,4 +28,33 @@ class Projects::CommitsController < Projects::ApplicationController
       end
     end
   end
+
+  def signatures
+    respond_to do |format|
+      format.json do
+        render json: {
+          signatures: @commits.select(&:has_signature?).map do |commit|
+            {
+              commit_sha: commit.sha,
+              html: view_to_html_string('projects/commit/_signature', signature: commit.signature)
+            }
+          end
+        }
+      end
+    end
+  end
+
+  private
+
+  def set_commits
+    @limit, @offset = (params[:limit] || 40).to_i, (params[:offset] || 0).to_i
+    search = params[:search]
+
+    @commits =
+      if search.present?
+        @repository.find_commits_by_message(search, @ref, @path, @limit, @offset)
+      else
+        @repository.commits(@ref, path: @path, limit: @limit, offset: @offset)
+      end
+  end
 end
diff --git a/app/controllers/projects/graphs_controller.rb b/app/controllers/projects/graphs_controller.rb
index 57372f9e79d..475d4c86294 100644
--- a/app/controllers/projects/graphs_controller.rb
+++ b/app/controllers/projects/graphs_controller.rb
@@ -43,23 +43,7 @@ class Projects::GraphsController < Projects::ApplicationController
   end
 
   def get_languages
-    @languages = Linguist::Repository.new(@repository.rugged, @repository.rugged.head.target_id).languages
-    total = @languages.map(&:last).sum
-
-    @languages = @languages.map do |language|
-      name, share = language
-      color = Linguist::Language[name].color || "##{Digest::SHA256.hexdigest(name)[0...6]}"
-      {
-        value: (share.to_f * 100 / total).round(2),
-        label: name,
-        color: color,
-        highlight: color
-      }
-    end
-
-    @languages.sort! do |x, y|
-      y[:value] <=> x[:value]
-    end
+    @languages = @project.repository.languages
   end
 
   def fetch_graph
diff --git a/app/controllers/projects/merge_requests_controller.rb b/app/controllers/projects/merge_requests_controller.rb
index 70c41da4de5..d361e661d0e 100644
--- a/app/controllers/projects/merge_requests_controller.rb
+++ b/app/controllers/projects/merge_requests_controller.rb
@@ -223,12 +223,18 @@ class Projects::MergeRequestsController < Projects::MergeRequests::ApplicationCo
             if can?(current_user, :read_environment, environment) && environment.has_metrics?
               metrics_project_environment_deployment_path(environment.project, environment, deployment)
             end
+          
+          metrics_monitoring_url = 
+            if can?(current_user, :read_environment, environment)
+              environment_metrics_path(environment)
+            end
 
           {
             id: environment.id,
             name: environment.name,
             url: project_environment_path(project, environment),
             metrics_url: metrics_url,
+            metrics_monitoring_url: metrics_monitoring_url,
             stop_url: stop_url,
             external_url: environment.external_url,
             external_url_formatted: environment.formatted_external_url,
diff --git a/app/controllers/projects/wikis_controller.rb b/app/controllers/projects/wikis_controller.rb
index ac98470c2b1..968d880886c 100644
--- a/app/controllers/projects/wikis_controller.rb
+++ b/app/controllers/projects/wikis_controller.rb
@@ -55,6 +55,9 @@ class Projects::WikisController < Projects::ApplicationController
     else
       render 'edit'
     end
+  rescue WikiPage::PageChangedError
+    @conflict = true
+    render 'edit'
   end
 
   def create
@@ -119,6 +122,6 @@ class Projects::WikisController < Projects::ApplicationController
   end
 
   def wiki_params
-    params.require(:wiki).permit(:title, :content, :format, :message)
+    params.require(:wiki).permit(:title, :content, :format, :message, :last_commit_sha)
   end
 end
diff --git a/app/controllers/projects_controller.rb b/app/controllers/projects_controller.rb
index db4ea9c7d27..5c7c99fe7ef 100644
--- a/app/controllers/projects_controller.rb
+++ b/app/controllers/projects_controller.rb
@@ -301,10 +301,10 @@ class ProjectsController < Projects::ApplicationController
 
   def project_params
     params.require(:project)
-      .permit(project_params_ce)
+      .permit(project_params_attributes)
   end
 
-  def project_params_ce
+  def project_params_attributes
     [
       :avatar,
       :build_allow_git_fetch,
diff --git a/app/controllers/sessions_controller.rb b/app/controllers/sessions_controller.rb
index 69513f4dadc..9e743685d60 100644
--- a/app/controllers/sessions_controller.rb
+++ b/app/controllers/sessions_controller.rb
@@ -23,12 +23,7 @@ class SessionsController < Devise::SessionsController
 
   def new
     set_minimum_password_length
-    @ldap_servers =
-      if Gitlab.config.ldap.enabled
-        Gitlab::LDAP::Config.servers
-      else
-        []
-      end
+    @ldap_servers = Gitlab::LDAP::Config.available_servers
 
     super
   end
diff --git a/app/controllers/users_controller.rb b/app/controllers/users_controller.rb
index 8131eba6a2f..4ee855806ab 100644
--- a/app/controllers/users_controller.rb
+++ b/app/controllers/users_controller.rb
@@ -73,10 +73,7 @@ class UsersController < ApplicationController
   end
 
   def calendar
-    calendar = contributions_calendar
-    @activity_dates = calendar.activity_dates
-
-    render 'calendar', layout: false
+    render json: contributions_calendar.activity_dates
   end
 
   def calendar_activities