class ApplicationController < ActionController::Base
include ArvadosApiClientHelper
+ include ApplicationHelper
respond_to :html, :json, :js
protect_from_forgery
ERROR_ACTIONS = [:render_error, :render_not_found]
around_filter :thread_clear
- around_filter :thread_with_mandatory_api_token, except: ERROR_ACTIONS
- around_filter :thread_with_optional_api_token
+ around_filter :set_thread_api_token
+ # Methods that don't require login should
+ # skip_around_filter :require_thread_api_token
+ around_filter :require_thread_api_token, except: ERROR_ACTIONS
before_filter :check_user_agreements, except: ERROR_ACTIONS
before_filter :check_user_notifications, except: ERROR_ACTIONS
- before_filter :find_object_by_uuid, except: [:index] + ERROR_ACTIONS
+ before_filter :find_object_by_uuid, except: [:index, :choose] + ERROR_ACTIONS
theme :select_theme
begin
- rescue_from Exception,
- :with => :render_exception
- rescue_from ActiveRecord::RecordNotFound,
- :with => :render_not_found
- rescue_from ActionController::RoutingError,
- :with => :render_not_found
- rescue_from ActionController::UnknownController,
- :with => :render_not_found
- rescue_from ::AbstractController::ActionNotFound,
- :with => :render_not_found
+ rescue_from(ActiveRecord::RecordNotFound,
+ ActionController::RoutingError,
+ ActionController::UnknownController,
+ AbstractController::ActionNotFound,
+ with: :render_not_found)
+ rescue_from(Exception,
+ ActionController::UrlGenerationError,
+ with: :render_exception)
end
def unprocessable(message=nil)
else
@errors = [e.to_s]
end
- self.render_error status: 422
+ if e.is_a? ArvadosApiClient::NotLoggedInException
+ self.render_error status: 422
+ else
+ set_thread_api_token do
+ self.render_error status: 422
+ end
+ end
end
def render_not_found(e=ActionController::RoutingError.new("Path not found"))
logger.error e.inspect
@errors = ["Path not found"]
- self.render_error status: 404
+ set_thread_api_token do
+ self.render_error status: 404
+ end
end
- def index
+ def find_objects_for_index
@limit ||= 200
if params[:limit]
@limit = params[:limit].to_i
end
@objects ||= model_class
- @objects = @objects.filter(@filters).limit(@limit).offset(@offset).all
+ @objects = @objects.filter(@filters).limit(@limit).offset(@offset)
+ end
+
+ def render_index
respond_to do |f|
f.json { render json: @objects }
- f.html { render }
+ f.html {
+ if params['tab_pane']
+ comparable = self.respond_to? :compare
+ render(partial: 'show_' + params['tab_pane'].downcase,
+ locals: { comparable: comparable, objects: @objects })
+ else
+ render
+ end
+ }
f.js { render }
end
end
+ def index
+ find_objects_for_index if !@objects
+ render_index
+ end
+
+ helper_method :next_page_offset
+ def next_page_offset
+ if @objects.respond_to?(:result_offset) and
+ @objects.respond_to?(:result_limit) and
+ @objects.respond_to?(:items_available)
+ next_offset = @objects.result_offset + @objects.result_limit
+ if next_offset < @objects.items_available
+ next_offset
+ else
+ nil
+ end
+ end
+ end
+
def show
if !@object
return render_not_found("object not found")
respond_to do |f|
f.json { render json: @object.attributes.merge(href: url_for(@object)) }
f.html {
- if request.method == 'GET'
+ if params['tab_pane']
+ comparable = self.respond_to? :compare
+ render(partial: 'show_' + params['tab_pane'].downcase,
+ locals: { comparable: comparable, objects: @objects })
+ elsif request.method.in? ['GET', 'HEAD']
render
else
redirect_to params[:return_to] || @object
end
end
+ def choose
+ params[:limit] ||= 40
+ if !@objects
+ if params[:project_uuid] and !params[:project_uuid].empty?
+ # We want the chooser to show objects of the controllers's model_class
+ # type within a specific project specified by project_uuid, so fetch the
+ # project and request the contents of the project filtered on the
+ # controllers's model_class kind.
+ @objects = Group.find(params[:project_uuid]).contents({:filters => [['uuid', 'is_a', "arvados\##{ArvadosApiClient.class_kind(model_class)}"]]})
+ end
+ find_objects_for_index if !@objects
+ end
+ respond_to do |f|
+ if params[:partial]
+ f.json {
+ render json: {
+ content: render_to_string(partial: "choose_rows.html",
+ formats: [:html],
+ locals: {
+ multiple: params[:multiple]
+ }),
+ next_page_href: @next_page_href
+ }
+ }
+ end
+ f.js {
+ render partial: 'choose', locals: {multiple: params[:multiple]}
+ }
+ end
+ end
+
def render_content
if !@object
return render_not_found("object not found")
end
def update
- @updates ||= params[@object.class.to_s.underscore.singularize.to_sym]
+ @updates ||= params[@object.resource_param_name.to_sym]
@updates.keys.each do |attr|
if @object.send(attr).is_a? Hash
if @updates[attr].is_a? String
@new_resource_attrs ||= params[model_class.to_s.underscore.singularize]
@new_resource_attrs ||= {}
@new_resource_attrs.reject! { |k,v| k.to_s == 'uuid' }
- @object ||= model_class.new @new_resource_attrs
+ @object ||= model_class.new @new_resource_attrs, params["options"]
+ if @object.save
+ respond_to do |f|
+ f.json { render json: @object.attributes.merge(href: url_for(@object)) }
+ f.html {
+ redirect_to @object
+ }
+ f.js { render }
+ end
+ else
+ self.render_error status: 422
+ end
+ end
+
+ # Clone the given object, merging any attribute values supplied as
+ # with a create action.
+ def copy
+ @new_resource_attrs ||= params[model_class.to_s.underscore.singularize]
+ @new_resource_attrs ||= {}
+ @object = @object.dup
+ @object.update_attributes @new_resource_attrs
+ if not @new_resource_attrs[:name] and @object.respond_to? :name
+ if @object.name and @object.name != ''
+ @object.name = "Copy of #{@object.name}"
+ else
+ @object.name = "Copy of unnamed #{@object.class_for_display.downcase}"
+ end
+ end
@object.save!
show
end
end
def current_user
+ return Thread.current[:user] if Thread.current[:user]
+
if Thread.current[:arvados_api_token]
- Thread.current[:user] ||= User.current
+ if session[:user]
+ if session[:user][:is_active] != true
+ Thread.current[:user] = User.current
+ else
+ Thread.current[:user] = User.new(session[:user])
+ end
+ else
+ Thread.current[:user] = User.current
+ end
else
logger.error "No API token in Thread"
return nil
end
def show_pane_list
- %w(Attributes Metadata JSON API)
+ %w(Attributes Advanced)
end
protected
+ def strip_token_from_path(path)
+ path.sub(/([\?&;])api_token=[^&;]*[&;]?/, '\1')
+ end
+
def redirect_to_login
respond_to do |f|
f.html {
- if request.method == 'GET'
- redirect_to arvados_api_client.arvados_login_url(return_to: request.url)
+ if request.method.in? ['GET', 'HEAD']
+ redirect_to arvados_api_client.arvados_login_url(return_to: strip_token_from_path(request.url))
else
flash[:error] = "Either you are not logged in, or your session has timed out. I can't automatically log you in and re-attempt this request."
redirect_to :back
if params[:uuid].empty?
@object = nil
else
- @object = model_class.find(params[:uuid])
+ if (model_class != Link and
+ resource_class_for_uuid(params[:uuid]) == Link)
+ @name_link = Link.find(params[:uuid])
+ @object = model_class.find(@name_link.head_uuid)
+ else
+ @object = model_class.find(params[:uuid])
+ end
end
else
@object = model_class.where(uuid: params[:uuid]).first
Rails.cache.delete_matched(/^request_#{Thread.current.object_id}_/)
end
- def thread_with_api_token(login_optional = false)
+ # Save the session API token in thread-local storage, and yield.
+ # This method also takes care of session setup if the request
+ # provides a valid api_token parameter.
+ # If a token is unavailable or expired, the block is still run, with
+ # a nil token.
+ def set_thread_api_token
+ # If an API token has already been found, pass it through.
+ if Thread.current[:arvados_api_token]
+ yield
+ return
+ end
+
begin
- try_redirect_to_login = true
- if params[:api_token]
- try_redirect_to_login = false
- Thread.current[:arvados_api_token] = params[:api_token]
- # Before copying the token into session[], do a simple API
- # call to verify its authenticity.
- if verify_api_token
- session[:arvados_api_token] = params[:api_token]
- if !request.format.json? and request.method == 'GET'
- # Repeat this request with api_token in the (new) session
- # cookie instead of the query string. This prevents API
- # tokens from appearing in (and being inadvisedly copied
- # and pasted from) browser Location bars.
- redirect_to request.fullpath.sub(%r{([&\?]api_token=)[^&\?]*}, '')
- else
- yield
- end
- else
- @errors = ['Invalid API token']
- self.render_error status: 401
- end
- elsif session[:arvados_api_token]
- # In this case, the token must have already verified at some
- # point, but it might have been revoked since. We'll try
- # using it, and catch the exception if it doesn't work.
- try_redirect_to_login = false
- Thread.current[:arvados_api_token] = session[:arvados_api_token]
- begin
- yield
- rescue ArvadosApiClient::NotLoggedInException
- try_redirect_to_login = true
+ # If there's a valid api_token parameter, use it to set up the session.
+ if (Thread.current[:arvados_api_token] = params[:api_token]) and
+ verify_api_token
+ session[:arvados_api_token] = params[:api_token]
+ u = User.current
+ session[:user] = {
+ uuid: u.uuid,
+ email: u.email,
+ first_name: u.first_name,
+ last_name: u.last_name,
+ is_active: u.is_active,
+ is_admin: u.is_admin,
+ prefs: u.prefs
+ }
+ if !request.format.json? and request.method.in? ['GET', 'HEAD']
+ # Repeat this request with api_token in the (new) session
+ # cookie instead of the query string. This prevents API
+ # tokens from appearing in (and being inadvisedly copied
+ # and pasted from) browser Location bars.
+ redirect_to strip_token_from_path(request.fullpath)
+ return
end
- else
- logger.debug "No token received, session is #{session.inspect}"
end
- if try_redirect_to_login
- unless login_optional
- redirect_to_login
- else
- # login is optional for this route so go on to the regular controller
+
+ # With setup done, handle the request using the session token.
+ Thread.current[:arvados_api_token] = session[:arvados_api_token]
+ begin
+ yield
+ rescue ArvadosApiClient::NotLoggedInException
+ # If we got this error with a token, it must've expired.
+ # Retry the request without a token.
+ unless Thread.current[:arvados_api_token].nil?
Thread.current[:arvados_api_token] = nil
yield
end
end
end
- def thread_with_mandatory_api_token
- thread_with_api_token do
- yield
- end
- end
-
- # This runs after thread_with_mandatory_api_token in the filter chain.
- def thread_with_optional_api_token
+ # Reroute this request if an API token is unavailable.
+ def require_thread_api_token
if Thread.current[:arvados_api_token]
- # We are already inside thread_with_mandatory_api_token.
yield
+ elsif session[:arvados_api_token]
+ # Expired session. Clear it before refreshing login so that,
+ # if this login procedure fails, we end up showing the "please
+ # log in" page instead of getting stuck in a redirect loop.
+ session.delete :arvados_api_token
+ redirect_to_login
else
- # We skipped thread_with_mandatory_api_token. Use the optional version.
- thread_with_api_token(true) do
- yield
- end
+ render 'users/welcome'
end
end
end
def check_user_agreements
- if current_user && !current_user.is_active && current_user.is_invited
+ if current_user && !current_user.is_active
+ if not current_user.is_invited
+ return render 'users/inactive'
+ end
signatures = UserAgreement.signatures
@signed_ua_uuids = UserAgreement.signatures.map &:head_uuid
@required_user_agreements = UserAgreement.all.map do |ua|
}
def check_user_notifications
+ return if params['tab_pane']
+
@notification_count = 0
@notifications = []
end
end
- helper_method :my_folders
- def my_folders
- return @my_folders if @my_folders
- @my_folders = []
+ helper_method :all_projects
+ def all_projects
+ @all_projects ||= Group.
+ filter([['group_class','in',['project','folder']]]).order('name')
+ end
+
+ helper_method :my_projects
+ def my_projects
+ return @my_projects if @my_projects
+ @my_projects = []
root_of = {}
- Group.filter([['group_class','=','folder']]).each do |g|
+ all_projects.each do |g|
root_of[g.uuid] = g.owner_uuid
- @my_folders << g
+ @my_projects << g
end
done = false
while not done
end
end
end
- @my_folders = @my_folders.select do |g|
+ @my_projects = @my_projects.select do |g|
root_of[g.uuid] == current_user.uuid
end
end
+ helper_method :projects_shared_with_me
+ def projects_shared_with_me
+ my_project_uuids = my_projects.collect &:uuid
+ all_projects.reject { |x| x.uuid.in? my_project_uuids }
+ end
+
+ helper_method :recent_jobs_and_pipelines
+ def recent_jobs_and_pipelines
+ (Job.limit(10) |
+ PipelineInstance.limit(10)).
+ sort_by do |x|
+ x.finished_at || x.started_at || x.created_at rescue x.created_at
+ end
+ end
+
+ helper_method :my_project_tree
+ def my_project_tree
+ build_project_trees
+ @my_project_tree
+ end
+
+ helper_method :shared_project_tree
+ def shared_project_tree
+ build_project_trees
+ @shared_project_tree
+ end
+
+ def build_project_trees
+ return if @my_project_tree and @shared_project_tree
+ parent_of = {current_user.uuid => 'me'}
+ all_projects.each do |ob|
+ parent_of[ob.uuid] = ob.owner_uuid
+ end
+ children_of = {false => [], 'me' => [current_user]}
+ all_projects.each do |ob|
+ if ob.owner_uuid != current_user.uuid and
+ not parent_of.has_key? ob.owner_uuid
+ parent_of[ob.uuid] = false
+ end
+ children_of[parent_of[ob.uuid]] ||= []
+ children_of[parent_of[ob.uuid]] << ob
+ end
+ buildtree = lambda do |children_of, root_uuid=false|
+ tree = {}
+ children_of[root_uuid].andand.each do |ob|
+ tree[ob] = buildtree.call(children_of, ob.uuid)
+ end
+ tree
+ end
+ sorted_paths = lambda do |tree, depth=0|
+ paths = []
+ tree.keys.sort_by { |ob|
+ ob.is_a?(String) ? ob : ob.friendly_link_name
+ }.each do |ob|
+ paths << {object: ob, depth: depth}
+ paths += sorted_paths.call tree[ob], depth+1
+ end
+ paths
+ end
+ @my_project_tree =
+ sorted_paths.call buildtree.call(children_of, 'me')
+ @shared_project_tree =
+ sorted_paths.call({'Shared with me' =>
+ buildtree.call(children_of, false)})
+ end
+
+ helper_method :get_object
+ def get_object uuid
+ if @get_object.nil? and @objects
+ @get_object = @objects.each_with_object({}) do |object, h|
+ h[object.uuid] = object
+ end
+ end
+ @get_object ||= {}
+ @get_object[uuid]
+ end
+
+ helper_method :project_breadcrumbs
+ def project_breadcrumbs
+ crumbs = []
+ current = @name_link || @object
+ while current
+ if current.is_a?(Group) and current.group_class.in?(['project','folder'])
+ crumbs.prepend current
+ end
+ if current.is_a? Link
+ current = Group.find?(current.tail_uuid)
+ else
+ current = Group.find?(current.owner_uuid)
+ end
+ end
+ crumbs
+ end
+
+ helper_method :current_project_uuid
+ def current_project_uuid
+ if @object.is_a? Group and @object.group_class.in?(['project','folder'])
+ @object.uuid
+ elsif @name_link.andand.tail_uuid
+ @name_link.tail_uuid
+ elsif @object and resource_class_for_uuid(@object.owner_uuid) == Group
+ @object.owner_uuid
+ else
+ nil
+ end
+ end
+
# helper method to get links for given object or uuid
helper_method :links_for_object
def links_for_object object_or_uuid
+ raise ArgumentError, 'No input argument' unless object_or_uuid
+ preload_links_for_objects([object_or_uuid])
uuid = object_or_uuid.is_a?(String) ? object_or_uuid : object_or_uuid.uuid
- preload_links_for_objects([uuid])
- @all_links_for[uuid]
+ @all_links_for[uuid] ||= []
end
# helper method to preload links for given objects and uuids
helper_method :preload_links_for_objects
def preload_links_for_objects objects_and_uuids
- uuids = objects_and_uuids.collect { |x| x.is_a?(String) ? x : x.uuid }
@all_links_for ||= {}
+
+ raise ArgumentError, 'Argument is not an array' unless objects_and_uuids.is_a? Array
+ return @all_links_for if objects_and_uuids.empty?
+
+ uuids = objects_and_uuids.collect { |x| x.is_a?(String) ? x : x.uuid }
+
+ # if already preloaded for all of these uuids, return
if not uuids.select { |x| @all_links_for[x].nil? }.any?
- # already preloaded for all of these uuids
- return
+ return @all_links_for
end
+
uuids.each do |x|
@all_links_for[x] = []
end
+
# TODO: make sure we get every page of results from API server
- Link.filter([['head_uuid','in',uuids]]).each do |link|
+ Link.filter([['head_uuid', 'in', uuids]]).each do |link|
@all_links_for[link.head_uuid] << link
end
+ @all_links_for
end
# helper method to get a certain number of objects of a specific type
# this can be used to replace any uses of: "dataclass.limit(n)"
- helper_method :get_objects_of_type
- def get_objects_of_type dataclass, size
- # if the objects_map has a value for this dataclass, and the size used
- # to retrieve those objects is greater than equal to size, return it
- size_key = "#{dataclass}_size"
- if @objects_map && @objects_map[dataclass] && @objects_map[size_key] &&
- (@objects_map[size_key] >= size)
- return @objects_map[dataclass]
+ helper_method :get_n_objects_of_class
+ def get_n_objects_of_class dataclass, size
+ @objects_map_for ||= {}
+
+ raise ArgumentError, 'Argument is not a data class' unless dataclass.is_a? ArvadosBase
+ raise ArgumentError, 'Argument is not a valid limit size' unless (size && size>0)
+
+ # if the objects_map_for has a value for this dataclass, and the
+ # size used to retrieve those objects is equal, return it
+ size_key = "#{dataclass.name}_size"
+ if @objects_map_for[dataclass.name] && @objects_map_for[size_key] &&
+ (@objects_map_for[size_key] == size)
+ return @objects_map_for[dataclass.name]
+ end
+
+ @objects_map_for[size_key] = size
+ @objects_map_for[dataclass.name] = dataclass.limit(size)
+ end
+
+ # helper method to get collections for the given uuid
+ helper_method :collections_for_object
+ def collections_for_object uuid
+ raise ArgumentError, 'No input argument' unless uuid
+ preload_collections_for_objects([uuid])
+ @all_collections_for[uuid] ||= []
+ end
+
+ # helper method to preload collections for the given uuids
+ helper_method :preload_collections_for_objects
+ def preload_collections_for_objects uuids
+ @all_collections_for ||= {}
+
+ raise ArgumentError, 'Argument is not an array' unless uuids.is_a? Array
+ return @all_collections_for if uuids.empty?
+
+ # if already preloaded for all of these uuids, return
+ if not uuids.select { |x| @all_collections_for[x].nil? }.any?
+ return @all_collections_for
+ end
+
+ uuids.each do |x|
+ @all_collections_for[x] = []
+ end
+
+ # TODO: make sure we get every page of results from API server
+ Collection.where(uuid: uuids).each do |collection|
+ @all_collections_for[collection.uuid] << collection
+ end
+ @all_collections_for
+ end
+
+ # helper method to get log collections for the given log
+ helper_method :log_collections_for_object
+ def log_collections_for_object log
+ raise ArgumentError, 'No input argument' unless log
+
+ preload_log_collections_for_objects([log])
+
+ uuid = log
+ fixup = /([a-f0-9]{32}\+\d+)(\+?.*)/.match(log)
+ if fixup && fixup.size>1
+ uuid = fixup[1]
+ end
+
+ @all_log_collections_for[uuid] ||= []
+ end
+
+ # helper method to preload collections for the given uuids
+ helper_method :preload_log_collections_for_objects
+ def preload_log_collections_for_objects logs
+ @all_log_collections_for ||= {}
+
+ raise ArgumentError, 'Argument is not an array' unless logs.is_a? Array
+ return @all_log_collections_for if logs.empty?
+
+ uuids = []
+ logs.each do |log|
+ fixup = /([a-f0-9]{32}\+\d+)(\+?.*)/.match(log)
+ if fixup && fixup.size>1
+ uuids << fixup[1]
+ else
+ uuids << log
+ end
+ end
+
+ # if already preloaded for all of these uuids, return
+ if not uuids.select { |x| @all_log_collections_for[x].nil? }.any?
+ return @all_log_collections_for
+ end
+
+ uuids.each do |x|
+ @all_log_collections_for[x] = []
+ end
+
+ # TODO: make sure we get every page of results from API server
+ Collection.where(uuid: uuids).each do |collection|
+ @all_log_collections_for[collection.uuid] << collection
end
+ @all_log_collections_for
+ end
+
+ # helper method to get object of a given dataclass and uuid
+ helper_method :object_for_dataclass
+ def object_for_dataclass dataclass, uuid
+ raise ArgumentError, 'No input argument dataclass' unless (dataclass && uuid)
+ preload_objects_for_dataclass(dataclass, [uuid])
+ @objects_for[uuid]
+ end
- @objects_map = {}
- @objects_map[dataclass] = dataclass.limit(size)
- @objects_map[size_key] = size
+ # helper method to preload objects for given dataclass and uuids
+ helper_method :preload_objects_for_dataclass
+ def preload_objects_for_dataclass dataclass, uuids
+ @objects_for ||= {}
- return @objects_map[dataclass]
+ raise ArgumentError, 'Argument is not a data class' unless dataclass.is_a? Class
+ raise ArgumentError, 'Argument is not an array' unless uuids.is_a? Array
+
+ return @objects_for if uuids.empty?
+
+ # if already preloaded for all of these uuids, return
+ if not uuids.select { |x| @objects_for[x].nil? }.any?
+ return @objects_for
+ end
+
+ dataclass.where(uuid: uuids).each do |obj|
+ @objects_for[obj.uuid] = obj
+ end
+ @objects_for
end
end
projects / arvados.git / blobdiff