Feature Request: Add getCodelistFromConceptSet() function for direct database query of concept sets

Currently, CodelistGenerator provides `codesFromConceptSet()` and `codesFromCohort()` functions that extract codelists from JSON files containing concept set expressions or cohort definitions.

We propose to expand the management of the `concept_sets` to the database. In some OMOP CDM setups (such as those managed by IOMED), `concept_sets` are stored directly in database tables (concept_set, concept_set_item, etc.) within the same database instance as the analysis data.

This feature request proposes adding a new function, `getCodelistFromConceptSet()`, that queries these database tables directly to build formal codelist objects, similar to how other functions in the package query vocabulary tables directly (e.g., getDrugIngredientCodes(), getICD10StandardCodes()).

## Rationale

• **Cleaner workflow:** Eliminates the need to export/import JSON files when concept sets are already stored natively in the database.
• **Consistency:** Aligns with the package's philosophy of direct database queries for vocabulary-based codelists.
• **Tested workflow:** At IOMED, we maintain concept sets in dedicated database tables within the OMOP instance, allowing for streamlined querying without intermediate file handling.
• **Efficiency:** Reduces overhead of JSON parsing and file I/O when database access is already available.

## Proposed Database Schema

The function would work with the OMOP CDM tables and a small extension:

```mermaid
erDiagram
concept_set ||--o{ concept_set_item : "has items"
concept ||--o{ concept_set_item : "is included in"
concept_set {
int concept_set_id PK
text concept_set_name
}
concept {
int concept_id PK
varchar concept_name
varchar domain_id
varchar vocabulary_id
varchar concept_class_id
varchar standard_concept
varchar concept_code
date valid_start_date
date valid_end_date
varchar invalid_reason
}
concept_set_item {
int concept_set_id PK,FK
int concept_id PK,FK
}
concept_class ||--o{ concept : "classifies"
domain ||--o{ concept : "belongs to"
vocabulary ||--o{ concept : "from"
```

## Proposed Function Signature and Implementation

See [OmopHelpers](https://github.com/iomedhealth/OmopHelpers) for the full implementation.

```r
getCodelistFromConceptSet <- function(conceptSetId, con, cdmSchema) {
# Point to the required tables in the database
concept_set_tbl <- dplyr::tbl(con, dbplyr::in_schema(cdmSchema, "concept_set"))
concept_set_item_tbl <- dplyr::tbl(con, dbplyr::in_schema(cdmSchema, "concept_set_item"))

# Retrieve the name of the concept set to use as the codelist name
codelistName <- concept_set_tbl |>
dplyr::filter(.data$concept_set_id == conceptSetId) |>
dplyr::pull("concept_set_name") |>
unique()

# Error handling: check if the concept set ID was found
if (length(codelistName) == 0) {
stop(glue::glue("No concept set found for concept_set_id: {conceptSetId}"))
}
# Warning if multiple names exist for the same ID
if (length(codelistName) > 1) {
warning(glue::glue("Multiple names found for concept_set_id: {conceptSetId}. Using the first one: '{codelistName[1]}'"))
codelistName <- codelistName[1]
}

codelistName <- clean_name(codelistName)

# Retrieve all unique concept IDs associated with the concept set ID
concept_ids <- concept_set_item_tbl |>
dplyr::filter(.data$concept_set_id == conceptSetId) |>
dplyr::pull("concept_id") |>
unique()

# Create a named list structure required by newCodelist
codelist <- list(concept_ids) |>
magrittr::set_names(codelistName)

# Return the formal, validated codelist object
return(omopgenerics::newCodelist(codelist))
}
```

## Implementation Details

The function would:

1. Query concept_set table: Retrieve the concept_set_name for the given conceptSetId to use as the codelist name.
2. Query concept_set_item table: Get all associated concept_ids for the concept set.
3. Name cleaning: Apply name standardization (e.g., via a clean_name() helper function).
4. Codelist creation: Build a named list and return an omopgenerics::newCodelist object.
5. Error handling: Validate that the concept set exists and handle edge cases like multiple names.

## Dependencies

• Requires omopgenerics package for newCodelist()
• Uses dplyr for database operations
• Assumes clean_name() helper function (could be added or use existing package utilities)

## Related Functions

• codesFromConceptSet(): Current JSON-based approach
• getDrugIngredientCodes(): Similar direct database querying pattern
• getICD10StandardCodes(): Another vocabulary table query function

## Testing Considerations

• Unit tests with mock database containing concept_set tables
• Integration tests with real OMOP CDM databases
• Edge case testing (missing concept sets, empty results, etc.)