Module: Bio::BaseSpace

Defined in:
lib/bio-basespace-sdk.rb,
lib/basespace/model.rb,
lib/basespace/model/file.rb,
lib/basespace/model/user.rb,
lib/basespace/api/base_api.rb,
lib/basespace/model/sample.rb,
lib/basespace/model/product.rb,
lib/basespace/model/project.rb,
lib/basespace/model/variant.rb,
lib/basespace/api/api_client.rb,
lib/basespace/model/coverage.rb,
lib/basespace/model/purchase.rb,
lib/basespace/api/billing_api.rb,
lib/basespace/model/genome_v1.rb,
lib/basespace/model/app_result.rb,
lib/basespace/api/basespace_api.rb,
lib/basespace/model/app_session.rb,
lib/basespace/model/application.rb,
lib/basespace/model/run_compact.rb,
lib/basespace/model/user_compact.rb,
lib/basespace/model/variant_info.rb,
lib/basespace/api/basespace_error.rb,
lib/basespace/model/file_response.rb,
lib/basespace/model/list_response.rb,
lib/basespace/model/resource_list.rb,
lib/basespace/model/user_response.rb,
lib/basespace/model/variant_header.rb,
lib/basespace/model/basespace_model.rb,
lib/basespace/model/genome_response.rb,
lib/basespace/model/response_status.rb,
lib/basespace/model/sample_response.rb,
lib/basespace/model/multipart_upload.rb,
lib/basespace/model/project_response.rb,
lib/basespace/model/query_parameters.rb,
lib/basespace/model/coverage_metadata.rb,
lib/basespace/model/coverage_response.rb,
lib/basespace/model/purchase_response.rb,
lib/basespace/model/purchased_product.rb,
lib/basespace/model/app_result_response.rb,
lib/basespace/model/app_session_compact.rb,
lib/basespace/model/application_compact.rb,
lib/basespace/model/app_session_response.rb,
lib/basespace/model/coverage_meta_response.rb,
lib/basespace/model/refund_purchase_response.rb,
lib/basespace/model/variants_header_response.rb,
lib/basespace/model/app_session_launch_object.rb,
lib/basespace/model/query_parameters_purchased_product.rb

Overview

BaseSpace Ruby SDK is to be used in the development of Apps and scripts for working with Illumina’s BaseSpace cloud-computing solution for next-gen sequencing data analysis.

Defined Under Namespace

Classes: APIClient, AppResult, AppResultResponse, AppSession, AppSessionCompact, AppSessionLaunchObject, AppSessionResponse, Application, ApplicationCompact, BaseAPI, BaseSpaceAPI, BaseSpaceModel, BillingAPI, Consumer, Coverage, CoverageMetaResponse, CoverageMetadata, CoverageResponse, File, FileResponse, GenomeResponse, GenomeV1, IllegalParameterError, ListResponse, Model, ModelNotInitializedError, MultipartUpload, NoResponseError, Product, Project, ProjectResponse, Purchase, PurchaseResponse, PurchasedProduct, QueryParameters, QueryParametersPurchasedProduct, RefundPurchaseResponse, ResourceList, ResponseStatus, RunCompact, Sample, SampleResponse, UndefinedParameterError, UnknownParameterError, UploadTask, User, UserCompact, UserResponse, Variant, VariantHeader, VariantInfo, VariantsHeaderResponse, WrongFiletypeError

Class Method Summary collapse

Class Method Details

.load_credentials ⇒ Object

Loads login and authentication credentials from a JSON file.

If the environment variable “BASESPACE_CREDENTIALS” is set, then the path to the JSON files is taken from there. Otherwise, the current directory is searched for the file “credentials.json”.

On success, returns a hash with the values for

  • client_id

  • client_secret

  • access_token

  • app_session_id

  • basespace_url

  • api_version

On failure, returns nil.



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# File 'lib/bio-basespace-sdk.rb', line 88

def self.load_credentials
  filename = "credentials.json"
  if ENV['BASESPACE_CREDENTIALS']
    jsonfile = ENV['BASESPACE_CREDENTIALS']
  else
    jsonfile = ::File.join('.', filename)
  end
  if ::File.exists?(jsonfile)
    hash = JSON.parse(::File.read(jsonfile))
    if $DEBUG
      $stderr.puts "    # ----- Bio::BaseSpace.load_credientials ----- "
      $stderr.puts "    # Loaded credentials from #{jsonfile}"
      $stderr.puts "    # "
    end
  else
    hash = nil
    $stderr.puts "    # ----- Bio::BaseSpace.load_credientials ----- "
    $stderr.puts "    # You can put your credentials for the BaseSpace in the"
    $stderr.puts "    #   #{jsonfile}"
    $stderr.puts "    # file or point to the file with an environmental variable"
    $stderr.puts "    #   export BASESPACE_CREDENTIALS=/path/to/your/#{filename}"
    $stderr.puts "    # in the following format:"
    data = {
      'client_id'       => '<your client id>',
      'client_secret'   => '<your client secret>',
      'access_token'    => '<your access token>',
      'app_session_id'  => '<app session id>',
      'basespace_url'   => 'https://api.basespace.illumina.com/',
      'api_version'     => 'v1pre3',
    }
    $stderr.puts JSON.pretty_generate(JSON.parse(data.to_json))
  end
  return hash
end