Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
end
def index
+ @objects = nil if !defined?(@objects)
find_objects_for_index if !@objects
render_index
end
end
def choose
+ @objects = nil if !defined?(@objects)
params[:limit] ||= 40
respond_to do |f|
if params[:partial]
def accept_uuid_as_id_param
- if params[:id] and params[:id].match /\D/
+ if params[:id] and params[:id].match(/\D/)
params[:uuid] = params.delete :id
end
end
helper_method :user_notifications
def user_notifications
+ @errors = nil if !defined?(@errors)
return [] if @errors or not current_user.andand.is_active or not Rails.configuration.show_user_notifications
@notifications ||= @@notification_tests.map do |t|
t.call(self, current_user)
helper_method :my_starred_projects
def my_starred_projects user
- return if @starred_projects
+ return if defined?(@starred_projects) && @starred_projects
links = Link.filter([['tail_uuid', '=', user.uuid],
['link_class', '=', 'star'],
['head_uuid', 'is_a', 'arvados#group']]).select(%w(head_uuid))
# That is: get toplevel projects under home, get subprojects of
# these projects, and so on until we hit the limit.
def my_wanted_projects(user, page_size=100)
- return @my_wanted_projects if @my_wanted_projects
+ return @my_wanted_projects if defined?(@my_wanted_projects) && @my_wanted_projects
from_top = []
uuids = [user.uuid]
end
def build_my_wanted_projects_tree(user, page_size=100)
- return @my_wanted_projects_tree if @my_wanted_projects_tree
+ return @my_wanted_projects_tree if defined?(@my_wanted_projects_tree) && @my_wanted_projects_tree
parent_of = {user.uuid => 'me'}
my_wanted_projects(user, page_size).each do |ob|
children_of[parent_of[ob.uuid]] ||= []
children_of[parent_of[ob.uuid]] << ob
end
- buildtree = lambda do |children_of, root_uuid=false|
+ buildtree = lambda do |chldrn_of, root_uuid=false|
tree = {}
- children_of[root_uuid].andand.each do |ob|
- tree[ob] = buildtree.call(children_of, ob.uuid)
+ chldrn_of[root_uuid].andand.each do |ob|
+ tree[ob] = buildtree.call(chldrn_of, ob.uuid)
end
tree
end
def remove_items
@removed_uuids = []
- links = []
params[:item_uuids].collect { |uuid| ArvadosBase.find uuid }.each do |item|
if item.class == Collection or item.class == Group
# Use delete API on collections and projects/groups
end
def current_api_host
- Rails.configuration.arvados_v1_base.gsub /https?:\/\/|\/arvados\/v1/,''
+ Rails.configuration.arvados_v1_base.gsub(/https?:\/\/|\/arvados\/v1/, '')
end
def current_uuid_prefix
def cwl_inputs_required(object, inputs_schema, set_attr_path)
r = 0
inputs_schema.each do |input|
- required, primary_type, param_id = cwl_input_info(input)
- dn, attrvalue = cwl_input_value(object, input, set_attr_path + [param_id])
+ required, _, param_id = cwl_input_info(input)
+ _, attrvalue = cwl_input_value(object, input, set_attr_path + [param_id])
r += 1 if required and attrvalue.nil?
end
r
private
def is_textile?( object, attr )
- is_textile = object.textile_attributes.andand.include?(attr)
+ object.textile_attributes.andand.include?(attr)
end
end
# For the benefit of themes that still expect $arvados_api_client to work:
class ArvadosClientProxyHack
def method_missing *args
- ArvadosApiClient.new_or_current.send *args
+ ArvadosApiClient.new_or_current.send(*args)
end
end
$arvados_api_client = ArvadosClientProxyHack.new
f0 = '' if f0 == '.'
f0 = f0[2..-1] if f0[0..1] == './'
f0 += '/' if not f0.empty?
- file_path = "#{f0}#{file[1]}"
+ "#{f0}#{file[1]}"
end
##
end
else
if step[:progress] and
- (re = step[:progress].match /^(\d+)\+(\d+)\/(\d+)$/)
+ (re = step[:progress].match(/^(\d+)\+(\d+)\/(\d+)$/))
pj[:progress] = (((re[1].to_f + re[2].to_f/2) / re[3].to_f) rescue 0.5)
else
pj[:progress] = 0.0
{label: 'output'})
end
# Input collection nodes
- output_pdhs = @opts[:output_collections].values.collect{|c|
- c[:portable_data_hash]}
+ output_pdhs = @opts[:output_collections].values.collect{|oc|
+ oc[:portable_data_hash]}
ProvenanceHelper::cr_input_pdhs(cr).each do |pdh|
if not output_pdhs.include?(pdh)
# Search for collections on the same project first
- cols = @opts[:input_collections][pdh].andand.select{|c|
- c[:owner_uuid] == cr[:owner_uuid]}
+ cols = @opts[:input_collections][pdh].andand.select{|ic|
+ ic[:owner_uuid] == cr[:owner_uuid]}
if not cols or cols.empty?
# Search for any collection with this PDH
cols = @opts[:input_collections][pdh]
end
def self.columns
+ @discovered_columns = [] if !defined?(@discovered_columns)
return @discovered_columns if @discovered_columns.andand.any?
- @discovered_columns = []
@attribute_info ||= {}
schema = arvados_api_client.discovery[:schemas][self.to_s.to_sym]
return @discovered_columns if schema.nil?
if opts[:class].is_a? Class
return opts[:class]
end
- if uuid.match /^[0-9a-f]{32}(\+[^,]+)*(,[0-9a-f]{32}(\+[^,]+)*)*$/
+ if uuid.match(/^[0-9a-f]{32}(\+[^,]+)*(,[0-9a-f]{32}(\+[^,]+)*)*$/)
return Collection
end
resource_class = nil
- uuid.match /^[0-9a-z]{5}-([0-9a-z]{5})-[0-9a-z]{15}$/ do |re|
+ uuid.match(/^[0-9a-z]{5}-([0-9a-z]{5})-[0-9a-z]{15}$/) do |re|
resource_class ||= arvados_api_client.
kind_class(self.uuid_infix_object_kind[re[1]])
end
if opts[:referring_object] and
opts[:referring_attr] and
- opts[:referring_attr].match /_uuid$/
+ opts[:referring_attr].match(/_uuid$/)
resource_class ||= arvados_api_client.
kind_class(opts[:referring_object].
attributes[opts[:referring_attr].
@fetch_multiple_pages = true
@arvados_api_token = Thread.current[:arvados_api_token]
@reader_tokens = Thread.current[:reader_tokens]
+ @results = nil
+ @count = nil
+ @offset = 0
+ @cond = nil
+ @eager = nil
+ @select = nil
+ @orderby_spec = nil
+ @filters = nil
+ @distinct = nil
+ @include_trash = nil
+ @limit = nil
end
def eager(bool=true)
end
end
end
- @cond.keys.select { |x| x.match /_kind$/ }.each do |kind_key|
+ @cond.keys.select { |x| x.match(/_kind$/) }.each do |kind_key|
if @cond[kind_key].is_a? Class
@cond = @cond.merge({ kind_key => 'arvados#' + arvados_api_client.class_kind(@cond[kind_key]) })
end
def each(&block)
if not @results.nil?
- @results.each &block
+ @results.each(&block)
else
self.each_page do |items|
items.each do |i|
@container = Container.find(container_uuid)
end
end
+ @container = nil if !defined?(@container)
@child_proxies = child_objects
end
} %>
</ul>
</li>
- <% if @name_link or @object %>
+ <% if (defined?(@name_link) && @name_link) or (defined?(@object) && @object) %>
<li class="nav-separator">
<i class="fa fa-lg fa-angle-double-right"></i>
</li>
<meta property="og:type" content="article" />
<meta property="og:url" content="<%= request.url %>" />
<meta property="og:site_name" content="<%= Rails.configuration.site_name %>" />
- <% if @object %>
+ <% if defined?(@object) && @object %>
<% if @object.respond_to?(:name) and @object.name.present? %>
<meta property="og:title" content="<%= @object.name%>" />
<% end %>
recent_cr_containers = recent_crs.map {|cr| cr.container_uuid}.compact.uniq
preload_objects_for_dataclass(Container, recent_cr_containers) if recent_cr_containers.andand.any?
- # fetch children of all the active crs in one call, if there are any
- active_crs = recent_crs.each {|cr| cr if (cr.priority.andand > 0 and cr.state != 'Final' and cr.container_uuid)}
-
wus = {}
outputs = []
recent_procs.each do |p|
# end
ActiveSupport::Inflector.inflections do |inflect|
- inflect.plural /^([Ss]pecimen)$/i, '\1s'
- inflect.singular /^([Ss]pecimen)s?/i, '\1'
- inflect.plural /^([Hh]uman)$/i, '\1s'
- inflect.singular /^([Hh]uman)s?/i, '\1'
+ inflect.plural(/^([Ss]pecimen)$/i, '\1s')
+ inflect.singular(/^([Ss]pecimen)s?/i, '\1')
+ inflect.plural(/^([Hh]uman)$/i, '\1s')
+ inflect.singular(/^([Hh]uman)s?/i, '\1')
end
%w(application.default application).each do |cfgfile|
path = "#{::Rails.root.to_s}/config/#{cfgfile}.yml"
- if File.exists? path
+ if File.exist? path
yaml = ERB.new(IO.read path).result(binding)
confs = YAML.load(yaml, deserialize_symbols: true)
$application_config.merge!(confs['common'] || {})
# exception if not found. Use this with assertions to explain that
# the error signifies a failed test rather than an unexpected error
# during a testing procedure.
- def find? *args
+ def find?(*args)
begin
- find *args
+ find(*args)
rescue Capybara::ElementNotFound
false
end
def after_teardown
if self.class.want_reset_api_fixtures[:after_each_test] and
- @want_reset_api_fixtures != false
+ (!defined?(@want_reset_api_fixtures) or @want_reset_api_fixtures != false)
self.class.reset_api_fixtures_now
end
super
PATH
remote: .
specs:
- arvados-login-sync (1.3.3.20190402172810)
+ arvados-login-sync (1.3.3.20190528194843)
arvados (~> 1.3.0, >= 1.3.0)
GEM
projects / arvados.git / commitdiff