Create siwaaenv

Create and initialize a Siwaa environment

createSiwaaEnv(
  SERVER = "https://siwaa.toulouse.inrae.fr",
  CARBOSEQ_TOOL_ID =
    "toolshed-siwaa.toulouse.inrae.fr/repos/patrick_chabrier/carboseq_s/CarboSeqSimulator/1.0.8",
  CARBOSEQ_WORKFLOW_ID = "32c9385265d8ab1a",
  API_KEY = Sys.getenv("CARBOSEQ_SIWAA_TOKEN"),
  INPUT_DIR = "../INPUTS/40Sites/csvdir",
  OUTPUT_DIR = "../OUTPUTS",
  HISTORY_ID = "4f93aea6ec2af23e",
  HISTORY_NAME = "CarboSeq [CarboSeqSimulator.R]",
  DELAY = 5,
  DURATION_MAX = 600,
  INVOCATION_DELAY = 10,
  INVOCATION_DURATION_MAX = 600,
  VERBOSE = FALSE
)

Arguments

SERVER

Siwaa server url (mandatory)

CARBOSEQ_TOOL_ID

'CarboSeqSimulator' tool id (default value for parameter of some methods)

CARBOSEQ_WORKFLOW_ID

'CarboSeqRun' workflow id (default value for parameter of some methods)

API_KEY

Available Siwaa API KEY (mandatory)

INPUT_DIR

Input folder containing the .csv input files (will be zipped) (default value for parameter of some methods)

OUTPUT_DIR

Folder destination of downloaded result file (default value for parameter of some methods)

HISTORY_ID

An existing history id (default value for parameter of some methods)

HISTORY_NAME

History name for a created history (default value for parameter of some methods)

DELAY

Delay (dataset survey). Unit : second. Default parameter value for 'waitSimsResults' method.

DURATION_MAX

Duration max (dataset survey). Unit : second. Default parameter value for 'waitSimsResults' method.

INVOCATION_DELAY

Delay (invocation survey). Unit : second. Default parameter value for some methods surveying workflow invocation state evolution ('runWorkflow', 'waitWorkflowOutputDataIdent').

INVOCATION_DURATION_MAX

Duration max (invocation survey). Unit : second. Default parameter value for some methods surveying workflow invocation state evolution ('waitWorkflowOutputDataIdent').

VERBOSE

Boolean to choose 'verbose' or 'silent' mode (default value for parameter of some methods)

Value

Siwaa environment

Details

siwaaenv contains some mandatory constants (SERVER, API_KEY) that must be verified and modified if necessary.

siwaaenv contains some constants (OUTPUT_DIR, CARBOSEQ_TOOL_ID, CARBOSEQ_WORKFLOW_ID, DURATION_MAX...) used as default values for some methods parameters : the user can choose to update them, or to give his own values by methods parameters. Example : setSiwaaEnv(..., DURATION_MAX=60) vs waitSimsResults(..., duration_max=60)

The method to update siwaaenv is setSiwaaEnv.

siwaaenv will be required by many methods as 'env' parameter.