Zarr Abstract Store

This class implements a Zarr abstract store. It provides the basic plumbing for specific implementations of a Zarr store. It implements the Zarr abstract store interface, with some extensions from the Python zarr.abc.store.Store abstract class. Functions set_partial_values() and get_partial_values() are not implemented.

References

https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#abstract-store-interface

Active bindings

friendlyClassName

(read-only) Name of the class for printing.

read_only

(read-only) Flag to indicate if the store is read-only.

supports_consolidated_metadata

Flag to indicate if the store can consolidate metadata.

supports_deletes

Flag to indicate if keys and arrays can be deleted.

supports_listing

Flag to indicate if the store can list its keys.

supports_partial_writes

Deprecated, always FALSE.

supports_writes

Flag to indicate if the store can write data.

version

(read-only) The Zarr version of the store.

separator

(read-only) The default separator between elements of chunks of arrays in the store. Every store typically has a default which is used when creating arrays. The actual chunk separator being used is determined by looking at the "chunk_key_encoding" attribute of each array.

Methods

Public methods

• zarr_store$new()

• zarr_store$clear()

• zarr_store$erase()

• zarr_store$erase_prefix()

• zarr_store$exists()

• zarr_store$get()

• zarr_store$getsize()

• zarr_store$getsize_prefix()

• zarr_store$is_empty()

• zarr_store$list()

• zarr_store$list_dir()

• zarr_store$list_prefix()

• zarr_store$set()

• zarr_store$set_if_not_exists()

• zarr_store$get_metadata()

• zarr_store$set_metadata()

• zarr_store$create_group()

• zarr_store$create_array()

---

Method new()

Create an instance of this class. Since this class is "abstract", it should not be instantiated directly - it is intended to be called by descendant classes, exclusively.

Usage

zarr_store$new(read_only = FALSE, version = 3L)

Arguments

read_only

Flag to indicate if the store is read-only. Default FALSE.

version

The version of the Zarr store. By default this is 3.

Returns

An instance of this class.

---

Method clear()

Clear the store. Remove all keys and values from the store.

Usage

zarr_store$clear()

Returns

Self, invisibly.

---

Method erase()

Remove a key from the store. This method is part of the abstract store interface in ZEP0001.

Usage

zarr_store$erase(key)

Arguments

key

Character string. The key to remove from the store.

Returns

Self, invisibly.

---

Method erase_prefix()

Remove all keys and prefixes in the store that begin with a given prefix. This method is part of the abstract store interface in ZEP0001.

Usage

zarr_store$erase_prefix(prefix)

Arguments

prefix

Character string. The prefix to groups or arrays to remove from the store, including in child groups.

Returns

Self, invisibly.

---

Method exists()

Check if a key exists in the store.

Usage

zarr_store$exists(key)

Arguments

key

Character string. The key that the store will be searched for.

Returns

TRUE if argument key is found, FALSE otherwise.

---

Method get()

Retrieve the value associated with a given key. This method is part of the abstract store interface in ZEP0001.

Usage

zarr_store$get(key, prototype, byte_range)

Arguments

key

Character string. The key for which to get data.

prototype

Ignored. The only buffer type that is supported maps directly to an R raw vector.

byte_range

If NULL, all data associated with the key is retrieved. If a single positive integer, all bytes starting from a given byte offset to the end of the object are returned. If a single negative integer, the final bytes are returned. If an integer vector of length 2, request a specific range of bytes where the end is exclusive. If the range ends after the end of the object, the entire remainder of the object will be returned. If the given range is zero-length or starts after the end of the object, an error will be returned.

Returns

An raw vector of data, or NULL if no data was found.

---

Method getsize()

Return the size, in bytes, of a value in a Store.

Usage

zarr_store$getsize(key)

Arguments

key

Character string. The key whose length will be returned.

Returns

The size, in bytes, of the object.

---

Method getsize_prefix()

Return the size, in bytes, of all objects found under the group indicated by the prefix.

Usage

zarr_store$getsize_prefix(prefix)

Arguments

prefix

Character string. The prefix to groups to scan.

Returns

The size, in bytes, of all the objects under a group, as a single integer value.

---

Method is_empty()

Is the group empty?

Usage

zarr_store$is_empty(prefix)

Arguments

prefix

Character string. The prefix to the group to scan.

Returns

TRUE is the group indicated by argument prefix has no sub-groups or arrays, FALSE otherwise.

---

Method list()

Retrieve all keys in the store. This method is part of the abstract store interface in ZEP0001.

Usage

zarr_store$list()

Returns

A character vector with all keys found in the store, both for groups and arrays.

---

Method list_dir()

Retrieve all keys and prefixes with a given prefix and which do not contain the character "/" after the given prefix. This method is part of the abstract store interface in ZEP0001.

Usage

zarr_store$list_dir(prefix)

Arguments

prefix

Character string. The prefix to groups to list.

Returns

A list with all keys found in the store immediately below the prefix, both for groups and arrays.

---

Method list_prefix()

Retrieve all keys and prefixes with a given prefix. This method is part of the abstract store interface in ZEP0001.

Usage

zarr_store$list_prefix(prefix)

Arguments

prefix

Character string. The prefix to groups to list.

Returns

A character vector with all fully-qualified keys found in the store, both for groups and arrays.

---

Method set()

Store a (key, value) pair.

Usage

zarr_store$set(key, value)

Arguments

key

The key whose value to set.

value

The value to set, typically a chunk of data.

Returns

Self, invisibly.

---

Method set_if_not_exists()

Store a key to argument value if the key is not already present. This method is part of the abstract store interface in ZEP0001.

Usage

zarr_store$set_if_not_exists(key, value)

Arguments

key

The key whose value to set.

value

The value to set, typically an R array.

Returns

Self, invisibly.

---

Method get_metadata()

Retrieve the metadata document of the node at the location indicated by the prefix argument.

Usage

zarr_store$get_metadata(prefix)

Arguments

prefix

The prefix of the node whose metadata document to retrieve.

---

Method set_metadata()

Set the metadata document of the node at the location indicated by the prefix argument. This is a no-op for stores that have no writing capability. Other stores must override this method.

Usage

zarr_store$set_metadata(prefix, metadata)

Arguments

prefix

The prefix of the node whose metadata document to set.

metadata

The metadata to persist, either a list or an instance of array_builder.

Returns

Self, invisible.

---

Method create_group()

Create a new group in the store under the specified path to the parent argument. The parent path must point to a Zarr group.

Usage

zarr_store$create_group(parent, name)

Arguments

parent

The path to the parent group of the new group.

name

The name of the new group.

Returns

A list with the metadata of the group, or an error if the group could not be created.

---

Method create_array()

Create a new array in the store under the specified path to the parent argument. The parent path must point to a Zarr group.

Usage

zarr_store$create_array(parent, name)

Arguments

parent

The path to the parent group of the new array.

name

The name of the new array.

Returns

A list with the metadata of the array, or an error if the array could not be created.