Function to execute a study task in Ulysses

Usage

execute_task(
  taskFile,
  configBlock,
  pipelineVersion = "dev",
  checkStatus = FALSE,
  env = rlang::caller_env(),
  codeState = NULL,
  logFilePath = NULL,
  cohortManifestHash = NULL,
  executionContext = NULL
)

Arguments

taskFile: the name of the taskFile. Only use the base name
configBlock: the name of the configBlock to use in the execution
pipelineVersion: the version of the pipeline to use in the execution. This is used to set the output folder for the task results. the default is "dev" which will place results in a dev folder. This allows users to run and test tasks without impacting the main results folders organized by pipeline version.
checkStatus: Logical. If TRUE, checks if task needs to be rerun based on file changes, dependencies, cohort changes, and previous errors. Automatically builds execution settings from configBlock. Default: FALSE
env: the execution environment
codeState: List or NULL. Working-tree provenance from runPreflightChecks() (sha and status). Recorded in exec/logs/task_run_history.csv alongside each run. NULL — the default, used when a task is run outside the pipeline — records the code state as "unrecorded" rather than implying a clean tree.
logFilePath: Character or NULL. Path to the pipeline log file for recording high-level milestones and full error detail. NULL (default) when run outside a pipeline (e.g. via testStudyTask()) — no file is written.
cohortManifestHash: Character or NULL. Pre-computed cohort manifest hash (see .getCohortManifestHash()). NULL (default) computes it once here; execute_pipeline() computes it once and passes it in so the manifest is not re-loaded for every task. Recorded with the run and used for the rerun check.
executionContext: An optional ExecutionContext for the current run. When supplied it owns namespace derivation (cohort-table suffix, results folder) and pipelineVersion is taken from it.