Zarr Store for HTTP access

This class implements a Zarr HTTP store. With this class Zarr stores on web servers can be read. For Zarr v.2 HTTP stores there exists a standard for publishing arrays on the store, using consolidated metadata. This class will look for such metadata in the root of the store. If no consolidated metadata is found then a regular group or array is searched for. Note that if a group is found that there is no standard process to determine what arrays are available in the store and where they are located relative to the root. Typically such information is found in the attributes of the group and you are advised to inspect those attributes and refer to the documentation of the store publisher.

This class performs no sanity checks on any of the arguments passed to the methods, for performance reasons. Since this class should be accessed through group and array objects, it is up to that code to ensure that arguments are valid, in particular keys and prefixes.

Super class

zarr::zarr_store -> zarr_httpstore

Active bindings

friendlyClassName

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

root

(read-only) The root of the HTTP store, identical to its URL.

uri

(read-only) The URI of the store location.

separator

(read-only) The default chunk separator of the store, usually a slash '/'.

Methods

Public methods

• zarr_httpstore$new()

• zarr_httpstore$exists()

• zarr_httpstore$clear()

• zarr_httpstore$erase()

• zarr_httpstore$erase_prefix()

• zarr_httpstore$list_dir()

• zarr_httpstore$list_prefix()

• zarr_httpstore$set()

• zarr_httpstore$set_if_not_exists()

• zarr_httpstore$get()

• zarr_httpstore$get_metadata()

• zarr_httpstore$set_metadata()

• zarr_httpstore$is_group()

• zarr_httpstore$create_group()

• zarr_httpstore$create_array()

Inherited methods

• zarr::zarr_store$getsize()
• zarr::zarr_store$getsize_prefix()
• zarr::zarr_store$is_empty()
• zarr::zarr_store$list()

---

Method new()

Create an instance of this class.

HTTP stores are read-only. Currently two types of Zarr store can be accessed. A Zarr v.2 consolidated metadata file at the root of the store (immediately below the URL) can identify a hierarchy of groups and arrays. Alternatively, a store with a group or a single array, either v.2 or v.3.

Usage

zarr_httpstore$new(url)

Arguments

url

The path to the HTTP store to be opened. The URL may use UTF-8 code points.

Returns

An instance of this class.

---

Method exists()

Check if a key exists in the store. The key can point to a group, an array, or a metadata file. This check is only relevant for HTTP stores with consolidated metadata. In other cases the single group or array will be at the root.

Usage

zarr_httpstore$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 clear()

Clearing the store is not supported.

Usage

zarr_httpstore$clear()

Returns

FALSE.

---

Method erase()

Removing a key from the store is not supported.

Usage

zarr_httpstore$erase(key)

Arguments

key

Ignored.

Returns

FALSE.

---

Method erase_prefix()

Removing keys from the store is not supported.

Usage

zarr_httpstore$erase_prefix(prefix)

Arguments

prefix

Ignored.

Returns

FALSE.

---

Method list_dir()

Retrieve all keys and prefixes with a given prefix and which do not contain the character "/" after the given prefix. In other words, this retrieves all the nodes in the store below the node indicated by the prefix.

Usage

zarr_httpstore$list_dir(prefix)

Arguments

prefix

Character string. The prefix whose nodes to list.

Returns

A character array 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.

Usage

zarr_httpstore$list_prefix(prefix)

Arguments

prefix

Character string. The prefix whose nodes to list.

Returns

A character vector with all paths found in the store below the prefix location, both for groups and arrays.

---

Method set()

Storing a (key, value) pair is not supported.

Usage

zarr_httpstore$set(key, value)

Arguments

key

Ignored.

value

Ignored.

Returns

Self, invisibly.

---

Method set_if_not_exists()

Storing a (key, value) pair is not supported.

Usage

zarr_httpstore$set_if_not_exists(key, value)

Arguments

key

Ignored.

value

Ignored.

Returns

Self, invisibly.

---

Method get()

Retrieve the value associated with a given key.

Usage

zarr_httpstore$get(key, prototype = NULL, byte_range = NULL)

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

Ignored. The full data value is always returned.

Returns

A raw vector with the data pointed at by the key.

---

Method get_metadata()

Retrieve the metadata document of the node at the location indicated by the prefix argument. The metadata will always be presented to the caller in the Zarr v.3 format. Attributes, if present, will be added.

Usage

zarr_httpstore$get_metadata(prefix)

Arguments

prefix

The prefix of the node whose metadata document to retrieve.

Returns

A list with the metadata, or NULL if the prefix is not pointing to a Zarr group or array.

---

Method set_metadata()

Setting metadata is not supported.

Usage

zarr_httpstore$set_metadata(prefix, metadata)

Arguments

prefix

Ignored.

metadata

Ignored.

Returns

Self, invisible

---

Method is_group()

Test if path is pointing to a Zarr group.

Usage

zarr_httpstore$is_group(path)

Arguments

path

The path to test.

Returns

TRUE if the path points to a Zarr group, FALSE otherwise.

---

Method create_group()

Creating a new group in the store is not supported.

Usage

zarr_httpstore$create_group(path, name)

Arguments

path, name

Ignored.

Returns

An error indicating that the group could not be created.

---

Method create_array()

Creating a new array in the store is not supported.

Usage

zarr_httpstore$create_array(parent, name, metadata)

Arguments

parent, name, metadata

Ignored.

Returns

An error indicating that the array could not be created.