From aadfe011b75c85e3bf943d997673033056d16311 Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Tue, 7 May 2024 08:29:04 -0400
Subject: [PATCH] zarr_open

---
 NAMESPACE                    |  1 +
 R/creation.R                 | 48 +++++++++++++++++++++++++++++++++++-
 man/zarr_open.Rd             | 29 ++++++++++++++++++++++
 pkgdown/_pkgdown.yml         |  1 +
 tests/testthat/test-compat.R | 10 ++++++++
 5 files changed, 88 insertions(+), 1 deletion(-)
 create mode 100644 man/zarr_open.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 557d5b8..ed7c1f6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -33,6 +33,7 @@ export(zarr_create_array)
 export(zarr_create_empty)
 export(zarr_create_group)
 export(zarr_create_zeros)
+export(zarr_open)
 export(zarr_open_array)
 export(zarr_open_group)
 export(zarr_save_array)
diff --git a/R/creation.R b/R/creation.R
index 60f6690..06f0fe9 100644
--- a/R/creation.R
+++ b/R/creation.R
@@ -790,4 +790,50 @@ zarr_save_array <- function(store, arr, ...) {
     # Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0e6cdc04c6413e14f57f61d389972ea937c/zarr/convenience.py#L112
     store <- normalize_store_arg(store)
     zarr_create_array(data=arr$get_item("..."), shape=arr$get_shape(), store=store, ...)
-}
\ No newline at end of file
+}
+
+#' Convenience function to open a group or array using file-mode-like semantics.
+#' @param store : MutableMapping or string, optional
+#'     Store or path to directory in file system or name of zip file.
+#' @param mode : {'r', 'r+', 'a', 'w', 'w-'}, optional
+#'     Persistence mode: 'r' means read only (must exist); 'r+' means
+#'     read/write (must exist); 'a' means read/write (create if doesn't
+#'     exist); 'w' means create (overwrite if exists); 'w-' means create
+#'     (fail if exists).
+#' @param path : str or NA, optional
+#'     The path within the store to open.
+#' @param ... Additional arguments to pass to zarr_open_array or zarr_open_group.
+#' @returns ZarrArray or ZarrGroup
+#' @export
+zarr_open <- function(store = NA, mode = NA, path = NA, ...) {
+    kwargs <- list(...)
+
+    if(is_na(mode)) {
+        mode <- "a"
+    }
+
+    store <- normalize_store_arg(store)
+    path <- normalize_storage_path(path)
+
+    if(mode %in% c("w", "w-", "x")) {
+        if("shape" %in% names(kwargs)) {
+            return(zarr_open_array(store=store, mode=mode, path=path, ...))
+        } else {
+            return(zarr_open_group(store=store, mode=mode, path=path, ...))
+        }
+    } else if(mode == "a") {
+        if("shape" %in% names(kwargs) || contains_array(store, path)) {
+            return(zarr_open_array(store=store, mode=mode, path=path, ...))
+        } else {
+            return(zarr_open_group(store=store, mode=mode, path=path, ...))
+        }
+    } else {
+        if(contains_array(store, path)) {
+            return(zarr_open_array(store=store, mode=mode, path=path, ...))
+        } else if(contains_group(store, path)) {
+            return(zarr_open_group(store=store, mode=mode, path=path, ...))
+        } else {
+            stop("PathNotFoundError(path)")
+        }
+    }
+}
diff --git a/man/zarr_open.Rd b/man/zarr_open.Rd
new file mode 100644
index 0000000..8133590
--- /dev/null
+++ b/man/zarr_open.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/creation.R
+\name{zarr_open}
+\alias{zarr_open}
+\title{Convenience function to open a group or array using file-mode-like semantics.}
+\usage{
+zarr_open(store = NA, mode = NA, path = NA, ...)
+}
+\arguments{
+\item{store}{: MutableMapping or string, optional
+Store or path to directory in file system or name of zip file.}
+
+\item{mode}{: {'r', 'r+', 'a', 'w', 'w-'}, optional
+Persistence mode: 'r' means read only (must exist); 'r+' means
+read/write (must exist); 'a' means read/write (create if doesn't
+exist); 'w' means create (overwrite if exists); 'w-' means create
+(fail if exists).}
+
+\item{path}{: str or NA, optional
+The path within the store to open.}
+
+\item{...}{Additional arguments to pass to zarr_open_array or zarr_open_group.}
+}
+\value{
+ZarrArray or ZarrGroup
+}
+\description{
+Convenience function to open a group or array using file-mode-like semantics.
+}
diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
index 4bcf255..357781c 100644
--- a/pkgdown/_pkgdown.yml
+++ b/pkgdown/_pkgdown.yml
@@ -62,6 +62,7 @@ reference:
   - zarr_create_zeros
   - zarr_create_array
   - zarr_create_group
+  - zarr_open
   - zarr_open_group
   - zarr_open_array
   - zarr_save_array
diff --git a/tests/testthat/test-compat.R b/tests/testthat/test-compat.R
index 1a6db28..1031e3f 100644
--- a/tests/testthat/test-compat.R
+++ b/tests/testthat/test-compat.R
@@ -10,6 +10,16 @@ test_that("Can open Zarr group using convenience function", {
     expect_equal(a$get_shape(), c(4))
 })
 
+test_that("Can open Zarr group or array using convenience function", {
+
+    root <- system.file("extdata", "fixtures", "v2", "data.zarr", package="pizzarr")
+    g <- zarr_open(root)
+    a <- zarr_open(root, path="1d.contiguous.lz4.i2")
+
+    expect_equal(class(g)[1], "ZarrGroup")
+    expect_equal(class(a)[1], "ZarrArray")
+})
+
 test_that("Can open Zarr group and read a 1D 2-byte integer array with LZ4 compression", {
 
     root <- system.file("extdata", "fixtures", "v2", "data.zarr", package="pizzarr")