Zarr Hierarchy node — zarr

This class implements a Zarr node. The node is an element in the hierarchy of the Zarr object. As per the Zarr specification, the node is either a group or an array. Thus, this class is the ancestor of the zarr_group and zarr_array classes. This class manages common features such as names, key, prefixes and paths, as well as the hierarchy between nodes and the zarr_store for persistent storage.

This class should never have to be instantiated or accessed directly. Instead, use instances of zarr_group or zarr_array. Function arguments are largely not checked, the group and array instances should do so prior to calling methods here. The big exception is checking the validity of node names.

Active bindings

name: (read-only) The name of the node.
parent: The parent of the node. For a root node this returns NULL, otherwise this zarr_group or zarr_array instance. CAUTION: Setting the parent of a node can invalidate the Zarr hierarchy - expert use only.
store: (read-only) The store of the node.
path: (read-only) The path of this node, relative to the root node of the hierarchy.
prefix: (read-only) The prefix of this node, relative to the root node of the hierarchy.
metadata: The metadata document of this node, a list. CAUTION: Setting a list that is not properly describing this object will render the object invalid.
attributes: (read-only) Retrieve the list of attributes of this object. Attributes can be added or modified with the set_attribute() method or removed with the delete_attributes() method.

Methods

`zarr_node$new()`

Initialize a new node in a Zarr hierarchy.

Usage

zarr_node$new(name, metadata, parent, store)

Arguments

name: The name of the node.
metadata: List with the metadata of the node.
parent: The parent node of this new node. Must be omitted when initializing a root node.
store: The store to persist data in. Ignored if a parent is specified.

`zarr_node$post_open()`

This method is called automatically after a Zarr store is opened to allow for operations after the full hierarchy has been established. This is a no-op here, descendant classes with specific requirements should implement this method.

Usage

zarr_node$post_open()

Returns

Self, invisibly.

`zarr_node$print_attributes()`

Print the metadata "attributes" to the console. Usually called by the zarr_group and zarr_array print() methods.

Usage

zarr_node$print_attributes(...)

Arguments

...: Arguments passed to embedded functions. Of particular interest is width = . to specify the maximum width of the columns.

`zarr_node$attribute()`

Retrieve a specific attribute by path.

Usage

zarr_node$attribute(name)

Arguments

name: The name (path) of the attribute to retrieve, using / as separator for nested attributes. Numeric path segments index into array attributes (1-based), e.g. "zarr_conventions/2/name" retrieves the name field of the second convention object.

Returns

The attribute value, or NULL if not found.

`zarr_node$set_attribute()`

Add an attribute to the metadata of the object. If an attribute name already exists, it will be overwritten.

Usage

zarr_node$set_attribute(name, value)

Arguments

name: The name of the attribute. The name may be a compound path, relative to the "attributes" entry in the metadata, using a slash "/" as path separator. Each of the elements in the path (between slashes) must begin with a letter and be composed of letters, digits, and underscores and can be at most 255 characters long. Missing path elements will be created.
value: The value of the attribute. This can be of any supported type, including a vector or list of values. In general, an attribute should be a character value, a numeric value, a logical value, or a short vector or list of any of these.

Returns

Self, invisibly.

`zarr_node$append_array_attribute()`

Append an attribute to an array in the metadata of the object. If an attribute name already exists, it will be overwritten.

Usage

zarr_node$append_array_attribute(name, value, after = NULL)

Arguments

name: The name of the attribute. The name may be a compound path, relative to the "attributes" entry in the metadata, using a slash "/" as path separator. Each of the elements in the path (between slashes) must begin with a letter and be composed of letters, digits, and underscores and can be at most 255 characters long. Missing path elements will be created.
value: The value of the attribute. This can be of any supported type, including a vector or list of values. In general, an attribute should be a character value, a numeric value, a logical value, or a short vector or list of any of these.
after: A subscript, after which value is to be appended. The default is NULL, meaning that value will be placed after the existing values. Specifying after = 0L will place value before the existing values.

Returns

Self, invisibly.

`zarr_node$delete_attribute()`

Delete an attribute or array element. If the attribute is not present, this method simply returns.

Usage

zarr_node$delete_attribute(name)

Arguments

name: Character. The name (path) of the attribute to delete, using / as separator for nested attributes, e.g. "first/second/my_att". The name is relative to the attributes entry in the metadata of the node. To target an element of a JSON array attribute, append the 1-based index as the path segment, e.g. "first/second/my_arr/2" to delete the second element in the array, or "first/second/my_arr/2/description" to delete only the description field inside it. This nesting can be arbitrarily deep, including over multiple JSON arrays.

Returns

Self, invisibly.

`zarr_node$save()`

Persist any edits to the group or array to the store.

Usage

zarr_node$save()