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,
  customize_history_name = 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)

customize_history_name

Option to ask for history name customization (default value FALSE : no customization)

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.