Hybrid local remote

.Rbuildignore

@@ -4,3 +4,5 @@
 ^\.github$
 ^LICENSE\.md$
 ^README\.Rmd$
+^doc$
+^Meta$

.gitignore

@@ -10,3 +10,5 @@ split_files.makeflow
 ._*
 .DS_Store
 inst/doc
+/doc/
+/Meta/

DESCRIPTION

@@ -13,7 +13,8 @@ Description: Provides access to a copy of the Human Cell Atlas, but with
     into a SingleCellExperiment object. 
 License: GPL-3
 Depends:
-    R (>= 4.2.0)
+    R (>= 4.2.0),
+    dbplyr (>= 2.3.0)
 Imports:
     dplyr,
     SummarizedExperiment,
@@ -23,17 +24,16 @@ Imports:
     glue,
     HDF5Array,
     DBI,
-    RSQLite,
-    rappdirs,
+    tools,
     httr,
     cli,
     assertthat,
     SeuratObject,
-    Seurat,
     methods,
     rlang,
     stats,
-    RPostgres
+    RPostgres,
+    RSQLite
 Suggests:
     here,
     stringr,
@@ -48,8 +48,7 @@ Suggests:
     tools,
     rmarkdown,
     knitr,
-    testthat,
-    dbplyr (>= 2.3.0)
+    testthat
 Biarch: true
 biocViews: 
     AssayDomain,
@@ -66,6 +65,6 @@ biocViews:
 Encoding: UTF-8
 RoxygenNote: 7.2.3
 LazyDataCompression: xz
-URL: https://github.com/stemangiola/CuratedAtlasQuery
-BugReports: https://github.com/stemangiola/CuratedAtlasQuery/issues
+URL: https://github.com/stemangiola/CuratedAtlasQueryR
+BugReports: https://github.com/stemangiola/CuratedAtlasQueryR/issues
 VignetteBuilder: knitr

NAMESPACE

@@ -3,15 +3,18 @@
 S3method(as.sparse,DelayedMatrix)
 export(get_SingleCellExperiment)
 export(get_metadata)
+export(get_metadata_local)
 export(get_seurat)
 importClassesFrom(SingleCellExperiment,SingleCellExperiment)
 importFrom(BiocGenerics,cbind)
 importFrom(DBI,dbConnect)
 importFrom(HDF5Array,HDF5RealizationSink)
 importFrom(HDF5Array,loadHDF5SummarizedExperiment)
 importFrom(RPostgres,Postgres)
+importFrom(RSQLite,SQLITE_RO)
+importFrom(RSQLite,SQLite)
 importFrom(S4Vectors,DataFrame)
-importFrom(Seurat,as.Seurat)
+importFrom(SeuratObject,as.Seurat)
 importFrom(SeuratObject,as.sparse)
 importFrom(SingleCellExperiment,SingleCellExperiment)
 importFrom(SingleCellExperiment,simplifyToSCE)
@@ -37,6 +40,7 @@ importFrom(glue,glue)
 importFrom(httr,GET)
 importFrom(httr,modify_url)
 importFrom(httr,parse_url)
+importFrom(httr,progress)
 importFrom(httr,stop_for_status)
 importFrom(httr,write_disk)
 importFrom(methods,as)
@@ -47,7 +51,7 @@ importFrom(purrr,map_int)
 importFrom(purrr,pmap_chr)
 importFrom(purrr,reduce)
 importFrom(purrr,transpose)
-importFrom(rappdirs,user_cache_dir)
 importFrom(rlang,.data)
 importFrom(stats,setNames)
 importFrom(tibble,column_to_rownames)
+importFrom(tools,R_user_dir)

R/query.R

@@ -299,14 +299,14 @@ sync_remote_file <- function(full_url, output_file, ...) {
 #' Returns the default cache directory
 #'
 #' @return A length one character vector.
-#' @importFrom rappdirs user_cache_dir
+#' @importFrom tools R_user_dir
 #' @noRd
 #'
 get_default_cache_dir <- function() {
-    file.path(
-        user_cache_dir(),
-        "hca_harmonised"
-    )
+    packageName() |>
+        R_user_dir(
+            "cache"
+        )
 }
 
 #' @importFrom SeuratObject as.sparse
@@ -323,7 +323,7 @@ as.sparse.DelayedMatrix <- function(x) {
 #' the samples in that data frame
 #'
 #' @inheritDotParams get_SingleCellExperiment
-#' @importFrom Seurat as.Seurat
+#' @importFrom SeuratObject as.Seurat
 #' @export
 #' @return A Seurat object containing the same data as a call to
 #'   get_SingleCellExperiment.
@@ -343,18 +343,19 @@ get_seurat <- function(...) {
 #'   connect to the metadata database. Possible parameters are described here:
 #'   https://rpostgres.r-dbi.org/reference/postgres.
 #' @return A lazy data.frame subclass containing the metadata. You can interact
-#'   with this object using most standard dplyr functions. However, it is
-#'   recommended that you use the %LIKE% operator for string matching, as most
-#'   stringr functions will not work.
+#'   with this object using most standard dplyr functions. For string matching, 
+#'   it is recommended that you use `stringr::str_like` to filter character
+#'   columns, as `stringr::str_match` will not work.
 #' @export
 #' @examples
 #' library(dplyr)
+#' library(stringr)
 #' filtered_metadata <- get_metadata() |>
 #'     filter(
 #'         ethnicity == "African" &
-#'             assay %LIKE% "%10x%" &
-#'             tissue == "lung parenchyma" &
-#'             cell_type %LIKE% "%CD4%"
+#'         str_like(assay, "%10x%") &
+#'         tissue == "lung parenchyma" &
+#'         str_like(cell_type, "%CD4%")
 #'     )
 #'
 #' @importFrom DBI dbConnect
@@ -364,7 +365,7 @@ get_seurat <- function(...) {
 get_metadata <- function(
     connection = list(
         dbname="metadata",
-        host="zki3lfhznsa.db.cloud.edu.au",
+        host="xwwtauhwze2.db.cloud.edu.au",
         port="5432",
         password="password",
         user="public_access"
@@ -376,3 +377,49 @@ get_metadata <- function(
         do.call(dbConnect, args=_) |>
         tbl("metadata")
 }
+
+
+#' Downloads an SQLite database of the Human Cell Atlas metadata to a local 
+#' cache, and then opens it as a data frame. It can then be filtered and 
+#' passed into [get_SingleCellExperiment()] 
+#' to obtain a [`SingleCellExperiment`](SingleCellExperiment::SingleCellExperiment-class)
+#'
+#' @param remote_url Optional character vector of length 1. An HTTP URL pointing
+#'   to the location of the sqlite database.
+#' @param 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
+#'   metadata.sqlite
+#' @return A lazy data.frame subclass containing the metadata. You can interact
+#'   with this object using most standard dplyr functions. For string matching, 
+#'   it is recommended that you use `stringr::str_like` to filter character
+#'   columns, as `stringr::str_match` will not work.
+#' @export
+#' @examples
+#' library(dplyr)
+#' filtered_metadata <- get_metadata_local() |>
+#'     filter(
+#'         ethnicity == "African" &
+#'             assay %LIKE% "%10x%" &
+#'             tissue == "lung parenchyma" &
+#'             cell_type %LIKE% "%CD4%"
+#'     )
+#'
+#' @importFrom DBI dbConnect
+#' @importFrom RSQLite SQLite SQLITE_RO
+#' @importFrom dplyr tbl
+#' @importFrom httr progress
+#'
+get_metadata_local <- function(
+    remote_url = "https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/metadata-sqlite/metadata.sqlite",
+    cache_directory = get_default_cache_dir()
+) {
+    sqlite_path <- file.path(cache_directory, "metadata.sqlite")
+    sync_remote_file(
+        remote_url,
+        sqlite_path,
+        progress(type = "down", con = stderr())
+    )
+    SQLite() |>
+        dbConnect(drv = _, dbname = sqlite_path, flags = SQLITE_RO) |>
+        tbl("metadata")
+}