Returns unharmonised metadata for selected datasets. — get_unharmonised

Various metadata fields are not common between datasets, so it does not make sense for these to live in the main metadata table. This function is a utility that allows easy fetching of this data if necessary.

get_unharmonised_dataset(
  dataset_id,
  cells = NULL,
  conn = dbConnect(drv = duckdb(), read_only = TRUE),
  remote_url = UNHARMONISED_URL,
  cache_directory = get_default_cache_dir()
)

Arguments

dataset_id: A character vector, where each entry is a dataset ID obtained from the $file_id column of the table returned from get_metadata()
cells: An optional character vector of cell IDs. If provided, only metadata for those cells will be returned.
conn: An optional DuckDB connection object. If provided, it will re-use the existing connection instead of opening a new one.
remote_url: Optional character vector of length 1. An HTTP URL pointing to the root URL under which all the unharmonised dataset files are located.
cache_directory: Optional character vector of length 1. A file path on your local system to a directory (not a file) that will be used to store the unharmonised metadata files.

Value

A named list, where each name is a dataset file ID, and each value is a "lazy data frame", ie a tbl.

Examples

# \donttest{
dataset <- "838ea006-2369-4e2c-b426-b2a744a2b02b"
harmonised_meta <- get_metadata() |> 
    dplyr::filter(file_id == dataset) |> dplyr::collect()
unharmonised_meta <- get_unharmonised_dataset(dataset)
#> Error in get_unharmonised_dataset(dataset): could not find function "get_unharmonised_dataset"
unharmonised_tbl <- dplyr::collect(unharmonised_meta[[dataset]])
#> Error in dplyr::collect(unharmonised_meta[[dataset]]): object 'unharmonised_meta' not found
dplyr::left_join(harmonised_meta, unharmonised_tbl, by=c("file_id", "cell_"))
#> Error in is.data.frame(y): object 'unharmonised_tbl' not found
# }