Reset Cohort Manifest

Cleans up cohort manifest data at one of three scopes. All destructive operations require the user to type "yes" at a confirmation prompt (disable with confirm = FALSE for scripted use).

Usage

resetCohortManifest(
  manifest = NULL,
  cohortsFolderPath = here::here("inputs/cohorts"),
  scope = c("derived", "manifest", "full"),
  executionSettings = NULL,
  archive = FALSE,
  confirm = TRUE
)

Arguments

manifest

A CohortManifest R6 object. Required for scope = "derived"; optional for other scopes (extracts path and settings automatically when provided).

cohortsFolderPath

Character. Path to the cohorts folder. Inferred from manifest when provided; otherwise defaults to here::here("inputs/cohorts").

scope

Character. One of "derived", "manifest", or "full". Defaults to "derived".

executionSettings

An ExecutionSettings object. Required for scope = "full" to drop OMOP cohort tables. If manifest is provided and already has settings attached, those are used automatically; this argument overrides them.

archive

Logical. For scope = "manifest", if TRUE (default), archives source files in json/ and sql/ to a timestamped directory instead of deleting them. Set to FALSE to delete without archiving.

confirm

Logical. If TRUE (default), the user must type "yes" to proceed. Set to FALSE for non-interactive use.

Value

Invisibly returns NULL.

Scope options

"derived"

Removes all derived cohort rows from the SQLite database (union, subset, complement, composite) and deletes the derived/ folder. Base cohorts (circe, custom) and their files are untouched. Use when rebuilding the derived pipeline with new parameters. Requires a live manifest object.

"manifest"

Deletes the SQLite database and the derived/ folder. Source files in json/ and sql/ are archived to a timestamped directory (unless archive = FALSE) and can be restored after initCohortManifest() using $addCirceCohort() or $addSqlCohort().

"full"

Deletes the SQLite database, derived/, json/, sql/, and cohortsLoad.csv. Also drops OMOP cohort tables from the database (requires executionSettings).