Merge remote-tracking branch 'upstream/master' into 24196-protected-variables

* upstream/master: (89 commits)
  Revert "Merge branch 'grpc-1.3.4' into 'master'"
  Return nil when looking up config for unknown LDAP provider
  Avoid crash when trying to parse string with invalid UTF-8 sequence
  Enable Gitaly by default in GitLab 9.3
  Don’t create comment on JIRA if link already exists
  Disable sub_group_issuables_spec.rb for mysql
  Fix math rendering on blob pages
  Add changelog
  Don't allow to pass a user to ProjectWiki#http_url_to_repo
  Revert "Merge branch '1937-https-clone-url-username' into 'master'
"
  Fix bottom padding for build page
  Fix /unsubscribe slash command creating extra todos
  Fix omniauth-google-oauth2 dependencies in Gemfile.lock
  Update looks job log
  'New issue'/'New merge request' dropdowns should show only projects with issues/merge requests feature enabled
  Fix spec for Members::AuthorizedDestroyService
  31616-add-uptime-of-gitlab-instance-in-admin-area
  Set head pipeline when creating merge requests
  Create a separate helper to check if we show particular tab on a search page
  Add performance deltas between app deployments on Merge Request widget
  ...

15 files changed, 213 insertions, 10 deletions

diff --git a/db/migrate/20160615191922_set_missing_stage_on_ci_builds.rb b/db/migrate/20160615191922_set_missing_stage_on_ci_builds.rb
index bd0463886bc..4d6a61bd614 100644
--- a/db/migrate/20160615191922_set_missing_stage_on_ci_builds.rb
+++ b/db/migrate/20160615191922_set_missing_stage_on_ci_builds.rb
@@ -1,3 +1,4 @@
+# rubocop:disable Migration/UpdateColumnInBatches
 class SetMissingStageOnCiBuilds < ActiveRecord::Migration
   include Gitlab::Database::MigrationHelpers
 
diff --git a/db/migrate/20160721081015_drop_and_readd_has_external_wiki_in_projects.rb b/db/migrate/20160721081015_drop_and_readd_has_external_wiki_in_projects.rb
index 1eb99feb40c..b2a2ce41391 100644
--- a/db/migrate/20160721081015_drop_and_readd_has_external_wiki_in_projects.rb
+++ b/db/migrate/20160721081015_drop_and_readd_has_external_wiki_in_projects.rb
@@ -1,3 +1,4 @@
+# rubocop:disable Migration/UpdateColumnInBatches
 class DropAndReaddHasExternalWikiInProjects < ActiveRecord::Migration
   include Gitlab::Database::MigrationHelpers
 
diff --git a/db/migrate/20160901141443_set_confidential_issues_events_on_webhooks.rb b/db/migrate/20160901141443_set_confidential_issues_events_on_webhooks.rb
index f1a1f001cb3..febd2c0e65e 100644
--- a/db/migrate/20160901141443_set_confidential_issues_events_on_webhooks.rb
+++ b/db/migrate/20160901141443_set_confidential_issues_events_on_webhooks.rb
@@ -1,3 +1,4 @@
+# rubocop:disable Migration/UpdateColumnInBatches
 class SetConfidentialIssuesEventsOnWebhooks < ActiveRecord::Migration
   include Gitlab::Database::MigrationHelpers
 
diff --git a/db/migrate/20160919144305_add_type_to_labels.rb b/db/migrate/20160919144305_add_type_to_labels.rb
index 66172bda6ff..2d2725ccf59 100644
--- a/db/migrate/20160919144305_add_type_to_labels.rb
+++ b/db/migrate/20160919144305_add_type_to_labels.rb
@@ -1,3 +1,4 @@
+# rubocop:disable Migration/UpdateColumnInBatches
 class AddTypeToLabels < ActiveRecord::Migration
   include Gitlab::Database::MigrationHelpers
 
diff --git a/db/migrate/20161018124658_make_project_owners_masters.rb b/db/migrate/20161018124658_make_project_owners_masters.rb
index a576bb7b622..fe11699c196 100644
--- a/db/migrate/20161018124658_make_project_owners_masters.rb
+++ b/db/migrate/20161018124658_make_project_owners_masters.rb
@@ -1,3 +1,4 @@
+# rubocop:disable Migration/UpdateColumnInBatches
 class MakeProjectOwnersMasters < ActiveRecord::Migration
   include Gitlab::Database::MigrationHelpers
 
diff --git a/db/migrate/20161227192806_rename_slack_and_mattermost_notification_services.rb b/db/migrate/20161227192806_rename_slack_and_mattermost_notification_services.rb
index 50ad7437227..c7cada6dfc5 100644
--- a/db/migrate/20161227192806_rename_slack_and_mattermost_notification_services.rb
+++ b/db/migrate/20161227192806_rename_slack_and_mattermost_notification_services.rb
@@ -1,3 +1,4 @@
+# rubocop:disable Migration/UpdateColumnInBatches
 class RenameSlackAndMattermostNotificationServices < ActiveRecord::Migration
   include Gitlab::Database::MigrationHelpers
 
diff --git a/db/migrate/20170320173259_migrate_assignees.rb b/db/migrate/20170320173259_migrate_assignees.rb
index 23e7500a32d..7b61e811317 100644
--- a/db/migrate/20170320173259_migrate_assignees.rb
+++ b/db/migrate/20170320173259_migrate_assignees.rb
@@ -1,6 +1,4 @@
-# See http://doc.gitlab.com/ce/development/migration_style_guide.html
-# for more information on how to write migrations for GitLab.
-
+# rubocop:disable Migration/UpdateColumnInBatches
 class MigrateAssignees < ActiveRecord::Migration
   include Gitlab::Database::MigrationHelpers
 
diff --git a/db/migrate/20170503140201_reschedule_project_authorizations.rb b/db/migrate/20170503140201_reschedule_project_authorizations.rb
new file mode 100644
index 00000000000..fa45adadbae
--- /dev/null
+++ b/db/migrate/20170503140201_reschedule_project_authorizations.rb
@@ -0,0 +1,44 @@
+# See http://doc.gitlab.com/ce/development/migration_style_guide.html
+# for more information on how to write migrations for GitLab.
+
+class RescheduleProjectAuthorizations < ActiveRecord::Migration
+  include Gitlab::Database::MigrationHelpers
+
+  DOWNTIME = false
+
+  disable_ddl_transaction!
+
+  class User < ActiveRecord::Base
+    self.table_name = 'users'
+  end
+
+  def up
+    offset = 0
+    batch = 5000
+    start = Time.now
+
+    loop do
+      relation = User.where('id > ?', offset)
+      user_ids = relation.limit(batch).reorder(id: :asc).pluck(:id)
+
+      break if user_ids.empty?
+
+      offset = user_ids.last
+
+      # This will schedule each batch 5 minutes after the previous batch was
+      # scheduled. This smears out the load over time, instead of immediately
+      # scheduling a million jobs.
+      Sidekiq::Client.push_bulk(
+        'queue' => 'authorized_projects',
+        'args' => user_ids.zip,
+        'class' => 'AuthorizedProjectsWorker',
+        'at' => start.to_i
+      )
+
+      start += 5.minutes
+    end
+  end
+
+  def down
+  end
+end
diff --git a/db/migrate/20170503140202_turn_nested_groups_into_regular_groups_for_mysql.rb b/db/migrate/20170503140202_turn_nested_groups_into_regular_groups_for_mysql.rb
new file mode 100644
index 00000000000..c67690642c9
--- /dev/null
+++ b/db/migrate/20170503140202_turn_nested_groups_into_regular_groups_for_mysql.rb
@@ -0,0 +1,123 @@
+# See http://doc.gitlab.com/ce/development/migration_style_guide.html
+# for more information on how to write migrations for GitLab.
+
+# This migration depends on code external to it. For example, it relies on
+# updating a namespace to also rename directories (uploads, GitLab pages, etc).
+# The alternative is to copy hundreds of lines of code into this migration,
+# adjust them where needed, etc; something which doesn't work well at all.
+class TurnNestedGroupsIntoRegularGroupsForMysql < ActiveRecord::Migration
+  include Gitlab::Database::MigrationHelpers
+
+  # Set this constant to true if this migration requires downtime.
+  DOWNTIME = false
+
+  def run_migration?
+    Gitlab::Database.mysql?
+  end
+
+  def up
+    return unless run_migration?
+
+    # For all sub-groups we need to give the right people access. We do this as
+    # follows:
+    #
+    # 1. Get all the ancestors for the current namespace
+    # 2. Get all the members of these namespaces, along with their higher access
+    #    level
+    # 3. Give these members access to the current namespace
+    Namespace.unscoped.where('parent_id IS NOT NULL').find_each do |namespace|
+      rows = []
+      existing = namespace.members.pluck(:user_id)
+
+      all_members_for(namespace).each do |member|
+        next if existing.include?(member[:user_id])
+
+        rows << {
+          access_level: member[:access_level],
+          source_id: namespace.id,
+          source_type: 'Namespace',
+          user_id: member[:user_id],
+          notification_level: 3, # global
+          type: 'GroupMember',
+          created_at: Time.current,
+          updated_at: Time.current
+        }
+      end
+
+      bulk_insert_members(rows)
+
+      # This method relies on the parent to determine the proper path.
+      # Because we reset "parent_id" this method will not return the right path
+      # when moving namespaces.
+      full_path_was = namespace.send(:full_path_was)
+
+      namespace.define_singleton_method(:full_path_was) { full_path_was }
+
+      namespace.update!(parent_id: nil, path: new_path_for(namespace))
+    end
+  end
+
+  def down
+    # There is no way to go back from regular groups to nested groups.
+  end
+
+  # Generates a new (unique) path for a namespace.
+  def new_path_for(namespace)
+    counter = 1
+    base = namespace.full_path.tr('/', '-')
+    new_path = base
+
+    while Namespace.unscoped.where(path: new_path).exists?
+      new_path = base + "-#{counter}"
+      counter += 1
+    end
+
+    new_path
+  end
+
+  # Returns an Array containing all the ancestors of the current namespace.
+  #
+  # This method is not particularly efficient, but it's probably still faster
+  # than using the "routes" table. Most importantly of all, it _only_ depends
+  # on the namespaces table and the "parent_id" column.
+  def ancestors_for(namespace)
+    ancestors = []
+    current = namespace
+
+    while current&.parent_id
+      # We're using find_by(id: ...) here to deal with cases where the
+      # parent_id may point to a missing row.
+      current = Namespace.unscoped.select([:id, :parent_id]).
+        find_by(id: current.parent_id)
+
+      ancestors << current.id if current
+    end
+
+    ancestors
+  end
+
+  # Returns a relation containing all the members that have access to any of
+  # the current namespace's parent namespaces.
+  def all_members_for(namespace)
+    Member.
+      unscoped.
+      select(['user_id', 'MAX(access_level) AS access_level']).
+      where(source_type: 'Namespace', source_id: ancestors_for(namespace)).
+      group(:user_id)
+  end
+
+  def bulk_insert_members(rows)
+    return if rows.empty?
+
+    keys = rows.first.keys
+
+    tuples = rows.map do |row|
+      row.map { |(_, value)| connection.quote(value) }
+    end
+
+    execute <<-EOF.strip_heredoc
+    INSERT INTO members (#{keys.join(', ')})
+    VALUES #{tuples.map { |tuple| "(#{tuple.join(', ')})" }.join(', ')}
+    EOF
+  end
+end
diff --git a/db/migrate/20170504182103_add_index_project_group_links_group_id.rb b/db/migrate/20170504182103_add_index_project_group_links_group_id.rb
new file mode 100644
index 00000000000..62bf641daa6
--- /dev/null
+++ b/db/migrate/20170504182103_add_index_project_group_links_group_id.rb
@@ -0,0 +1,19 @@
+# See http://doc.gitlab.com/ce/development/migration_style_guide.html
+# for more information on how to write migrations for GitLab.
+
+class AddIndexProjectGroupLinksGroupId < ActiveRecord::Migration
+  include Gitlab::Database::MigrationHelpers
+
+  # Set this constant to true if this migration requires downtime.
+  DOWNTIME = false
+
+  disable_ddl_transaction!
+
+  def up
+    add_concurrent_index :project_group_links, :group_id
+  end
+
+  def down
+    remove_concurrent_index :project_group_links, :group_id
+  end
+end
diff --git a/db/post_migrate/20170131214021_reset_users_authorized_projects_populated.rb b/db/post_migrate/20170131214021_reset_users_authorized_projects_populated.rb
index b518038e93a..82f8147547e 100644
--- a/db/post_migrate/20170131214021_reset_users_authorized_projects_populated.rb
+++ b/db/post_migrate/20170131214021_reset_users_authorized_projects_populated.rb
@@ -1,6 +1,4 @@
-# See http://doc.gitlab.com/ce/development/migration_style_guide.html
-# for more information on how to write migrations for GitLab.
-
+# rubocop:disable Migration/UpdateColumnInBatches
 class ResetUsersAuthorizedProjectsPopulated < ActiveRecord::Migration
   include Gitlab::Database::MigrationHelpers
 
diff --git a/db/post_migrate/20170309171644_reset_relative_position_for_issue.rb b/db/post_migrate/20170309171644_reset_relative_position_for_issue.rb
index b61dd7cfc61..b1c9eed1148 100644
--- a/db/post_migrate/20170309171644_reset_relative_position_for_issue.rb
+++ b/db/post_migrate/20170309171644_reset_relative_position_for_issue.rb
@@ -1,6 +1,4 @@
-# See http://doc.gitlab.com/ce/development/migration_style_guide.html
-# for more information on how to write migrations for GitLab.
-
+# rubocop:disable Migration/UpdateColumnInBatches
 class ResetRelativePositionForIssue < ActiveRecord::Migration
   include Gitlab::Database::MigrationHelpers
 
diff --git a/db/post_migrate/20170502070007_enable_auto_cancel_pending_pipelines_for_all.rb b/db/post_migrate/20170502070007_enable_auto_cancel_pending_pipelines_for_all.rb
index a19b73fc114..3c13a3d2518 100644
--- a/db/post_migrate/20170502070007_enable_auto_cancel_pending_pipelines_for_all.rb
+++ b/db/post_migrate/20170502070007_enable_auto_cancel_pending_pipelines_for_all.rb
@@ -1,3 +1,4 @@
+# rubocop:disable Migration/UpdateColumnInBatches
 class EnableAutoCancelPendingPipelinesForAll < ActiveRecord::Migration
   include Gitlab::Database::MigrationHelpers
 
diff --git a/db/post_migrate/20170503120310_remove_users_authorized_projects_populated.rb b/db/post_migrate/20170503120310_remove_users_authorized_projects_populated.rb
new file mode 100644
index 00000000000..1b44334395f
--- /dev/null
+++ b/db/post_migrate/20170503120310_remove_users_authorized_projects_populated.rb
@@ -0,0 +1,15 @@
+# See http://doc.gitlab.com/ce/development/migration_style_guide.html
+# for more information on how to write migrations for GitLab.
+
+class RemoveUsersAuthorizedProjectsPopulated < ActiveRecord::Migration
+  include Gitlab::Database::MigrationHelpers
+
+  # Set this constant to true if this migration requires downtime.
+  DOWNTIME = false
+
+  disable_ddl_transaction!
+
+  def change
+    remove_column :users, :authorized_projects_populated, :boolean
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index 43bd50dce90..59f4e4b2961 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -929,6 +929,8 @@ ActiveRecord::Schema.define(version: 20170524161101) do
     t.date "expires_at"
   end
 
+  add_index "project_group_links", ["group_id"], name: "index_project_group_links_on_group_id", using: :btree
+
   create_table "project_import_data", force: :cascade do |t|
     t.integer "project_id"
     t.text "data"
@@ -1356,7 +1358,6 @@ ActiveRecord::Schema.define(version: 20170524161101) do
     t.boolean "external", default: false
     t.string "incoming_email_token"
     t.string "organization"
-    t.boolean "authorized_projects_populated"
     t.boolean "require_two_factor_authentication_from_group", default: false, null: false
     t.integer "two_factor_grace_period", default: 48, null: false
     t.boolean "ghost"