class Bio::BaseSpace::Sample
Public Class Methods
new()
click to toggle source
Return a new Sample
instance.
# File lib/basespace/model/sample.rb, line 25 def initialize @swagger_types = { 'HrefGenome' => 'str', 'SampleNumber' => 'int', 'ExperimentName' => 'str', 'HrefFiles' => 'str', 'AppSession' => 'dict', 'IsPairedEnd' => 'bool', 'Read1' => 'int', 'Read2' => 'int', 'NumReadsRaw' => 'int', 'NumReadsPF' => 'int', 'Id' => 'str', 'Href' => 'str', 'UserOwnedBy' => 'UserCompact', 'Name' => 'str', 'SampleId' => 'str', 'Status' => 'str', 'StatusSummary' => 'str', 'DateCreated' => 'datetime', 'References' => 'dict', # NOTE Is this correct? Because references is a list. 'Run' => 'RunCompact', } @attributes = { 'Name' => nil, # str 'HrefFiles' => nil, # str 'AppSession' => nil, # dict 'DateCreated' => nil, # datetime 'SampleNumber' => nil, # int 'Id' => nil, # str 'Href' => nil, # str 'UserOwnedBy' => nil, # UserCompact 'ExperimentName' => nil, # str 'Run' => nil, # RunCompact 'HrefGenome' => nil, # str 'IsPairedEnd' => nil, # bool 'Read1' => nil, # int 'Read2' => nil, # int 'NumReadsRaw' => nil, # int 'NumReadsPF' => nil, # int 'References' => nil, # dict 'SampleId' => nil, # dict 'Status' => nil, # dict 'StatusSummary' => nil, # dict } end
Public Instance Methods
get_access_str(scope = 'write')
click to toggle source
Returns the scope-string to be used for requesting BaseSpace
access to the sample.
scope
-
The scope type that is requested (write|read).
# File lib/basespace/model/sample.rb, line 91 def get_access_str(scope = 'write') is_init return scope + ' sample ' + get_attr('Id').to_s end
get_files(api, my_qp = {})
click to toggle source
Returns a list of File
objects.
api
-
BaseSpaceAPI
instance. my_qp
-
Query parameters to sort and filter the file list by.
# File lib/basespace/model/sample.rb, line 118 def get_files(api, my_qp = {}) is_init query_pars = QueryParameters.new(my_qp) return api.get_files_by_sample(get_attr('Id'), query_pars) end
get_referenced_app_results(api)
click to toggle source
Return the AppResults referenced by this sample.
Note: the returned AppResult
objects do not have their “References” field set, to get a fully populate AppResult
object you must use get_app_result_by_id in BaseSpaceAPI
.
api
-
BaseSpaceAPI
instance.
# File lib/basespace/model/sample.rb, line 102 def get_referenced_app_results(api) res = [] get_attr('References').each do |s| if s[:type] == 'AppResult' json_app_result = s[:content] my_ar = api.serialize_object(json_app_result, 'AppResult') res << my_ar end end return res end
is_init()
click to toggle source
Test if the sample instance has been initialized.
Throws ModelNotInitializedError
, if the Id variable is not set.
# File lib/basespace/model/sample.rb, line 80 def is_init raise ModelNotInitializedError.new('The sample model has not been initialized yet') unless get_attr('Id') end
to_s()
click to toggle source
Return the name of the sample.
# File lib/basespace/model/sample.rb, line 73 def to_s return get_attr('Name') end