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Migrate Old CohortManifest SQLite to New Schema

Source: R/migrateCohortManifest.R
migrateCohortManifest.Rd

One-time migration utility that converts an existing cohortManifest.sqlite (picard <= 0.0.3) to the new schema with category, source_type, cohort_type, depends_on, dependency_rule, and timestamp columns.

Usage

migrateCohortManifest(
  dbPath = "inputs/cohorts/cohortManifest.sqlite",
  categoryMap = NULL
)

Arguments

dbPath

Character. Path to the existing cohortManifest.sqlite file. Defaults to "inputs/cohorts/cohortManifest.sqlite".

categoryMap

Named list. Maps cohort labels to categories. Example: list("Type 2 Diabetes" = "target", "GI Bleed" = "outcome"). Cohorts not in the map will be assigned from tag keywords or "unclassified".

Value

Invisible tibble of migrated rows with their assigned categories.

Details

The migration performs the following steps:

  1. Backs up the old database to cohortManifest_backup_{timestamp}.sqlite

  2. Reads all rows from the old schema

  3. Infers source_type from file path (json/ -> "circe", sql/ -> "sql", derived/ -> "derived")

  4. Infers cohort_type from old cohortType column

  5. Assigns category from categoryMap, tag keywords, or defaults to "unclassified"

  6. Converts tags from pipe-delimited string to JSON named list

  7. Reads sidecar .json metadata for dependent cohorts -> dependency_rule and depends_on

  8. Creates new schema with unique indexes

  9. Inserts migrated rows

  10. Prints migration summary