Load Concept Set Manifest

Loads or creates a concept set manifest from CIRCE JSON files located in the inputs/conceptSets/json folder. The manifest is stored in an SQLite database for efficient querying and metadata persistence. ExecutionSettings are optional and only required if you plan to extract source codes or access vocabularies.

Usage

loadConceptSetManifest(
  conceptSetsFolderPath = here::here("inputs/conceptSets"),
  executionSettings = NULL
)

Arguments

conceptSetsFolderPath

Character. Path to the conceptSets folder containing the manifest database. Defaults to "inputs/conceptSets".

executionSettings

ExecutionSettings object. Optional. Defaults to NULL. Only required for operations like extractSourceCodes(). You can add settings later using setExecutionSettings() on the returned ConceptSetManifest object.

Value

ConceptSetManifest object containing all loaded concept sets with metadata.

Details

Workflow:

1. Checks if conceptSetManifest.sqlite database exists

2. If it exists, loads concept set entries from the json/ directory using cached metadata

3. If not, scans the json/ directory for CIRCE JSON files

4. Creates ConceptSetDef objects for each JSON file

5. Enriches metadata from conceptSetsLoad.csv if available

6. Returns a ConceptSetManifest object

Metadata CSV Format: The conceptSetsLoad.csv file (optional) should contain:

• file_name: Relative path to JSON file (e.g., "conceptSet1.json")

• label: Display name for the concept set

• atlasId: ATLAS concept set ID

• domain: OMOP domain classification

• sourceCode: Whether the concept set represents source codes

Post-Load: After loading, use manifest methods to query concept sets:

• getConceptSetById(id) - Get by database ID

• getConceptSetsByTag(key, value) - Get by metadata tag

• grabConceptSetById(id) - Get ConceptSetDef object

Examples

if (FALSE) {
  # Load concept set manifest (no settings required for metadata review)
  manifest <- loadConceptSetManifest()
  
  # Or load from custom path
  manifest <- loadConceptSetManifest(conceptSetsFolderPath = "path/to/conceptsets")
  
  # Add execution settings later if needed for source code extraction
  settings <- createExecutionSettings(
    connectionString = "Server=localhost;Database=mydb"
  )
  manifest$setExecutionSettings(settings)
  manifest$extractSourceCodes(sourceVocabs = c("ICD10CM"))
}