improve the counts database structure

Author: myushen

R/counts.R

@@ -112,7 +112,7 @@ get_single_cell_experiment <- function(
         has_name(raw_data, c("cell_", "file_id_db"))
     )
 
-    versioned_cache_directory <- file.path(cache_directory, COUNTS_VERSION)
+    versioned_cache_directory <- cache_directory
     versioned_cache_directory |> dir.create(
         showWarnings = FALSE,
         recursive = TRUE

R/unharmonised.R

@@ -54,7 +54,6 @@ get_unharmonised_dataset <- function(
 ){
     unharmonised_root <- file.path(
       cache_directory,
-      COUNTS_VERSION,
       "unharmonised"
     )
     file_name <- glue::glue("{dataset_id}.parquet")

R/utils.R

@@ -41,7 +41,7 @@ single_line_str <- function(text){
     str_remove_all(text, r"(\n\s*)")
 }
 
-#' Returns the default cache directory
+#' Returns the default cache directory with a version number
 #' @return A length one character vector.
 #' @importFrom tools R_user_dir
 #' @importFrom utils packageName
@@ -51,6 +51,7 @@ get_default_cache_dir <- function() {
         R_user_dir(
             "cache"
         ) |>
+        file.path(COUNTS_VERSION) |>
         normalizePath() |>
         suppressWarnings()
 }

tests/testthat/test-query.R

@@ -131,7 +131,7 @@ test_that("get_SingleCellExperiment() assigns the right cell ID to each cell", {
 
     # Load the SCE from cache directly
     assay_1 = CuratedAtlasQueryR:::get_default_cache_dir() |>
-        file.path(CuratedAtlasQueryR:::COUNTS_VERSION, "original", id) |>
+        file.path("original", id) |>
         HDF5Array::loadHDF5SummarizedExperiment() |>
         assay("X") |>
         as.matrix()