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AbstractWrapper Class

Source: R/wrappers.R
AbstractWrapper.Rd

Abstract class representing a local dataset object in a Vitessce dataset.

Details

Abstract dataset object wrapper class

Public fields

out_dir

The directory for processed output files.

use_cache

If converted output files already exist, should they be used?

is_remote

Is the data object fully remote?

routes

A list of VitessceConfigServerRoute objects.

file_def_creators

A list of file definition creator functions.

base_dir

The base directory for local data.

Methods

Public methods

Method new()

Create an abstract wrapper around a data object.

Usage

AbstractWrapper$new(out_dir = NA, use_cache = FALSE)

Arguments

out_dir

The directory for processed output files.

use_cache

If converted output files already exist, should they be used? By default, FALSE.

Returns

A new AbstractWrapper object.

Method convert_and_save()

Fill in the file_def_creators array. Each function added to this list should take in a base URL and generate a Vitessce file definition. If this wrapper is wrapping local data, then create routes and fill in the routes array. This method is void, should not return anything.

Usage

AbstractWrapper$convert_and_save(dataset_uid, obj_i, base_dir = NA)

Arguments

dataset_uid

A unique identifier for this dataset.

obj_i

Within the dataset, the index of this data wrapper object.

base_dir

Path to a base directory.

Method get_routes()

Obtain the routes that have been created for this wrapper class.

Usage

AbstractWrapper$get_routes()

Returns

A list of server routes.

Method get_file_defs()

Obtain the file definitions for this wrapper class.

Usage

AbstractWrapper$get_file_defs(base_url)

Arguments

base_url

A base URL to prepend to relative URLs.

Returns

A list of server routes.

Method get_out_dir_route()

Create a web server route for this object.

Usage

AbstractWrapper$get_out_dir_route(dataset_uid, obj_i)

Arguments

dataset_uid

The ID for this dataset.

obj_i

The index of this data object within the dataset.

Returns

A new VitessceConfigServerStaticRoute instance.

Method get_local_dir_url()

Construct a URL to a local directory.

Usage

AbstractWrapper$get_local_dir_url(
  base_url,
  dataset_uid,
  obj_i,
  local_dir_path,
  local_dir_uid
)

Arguments

base_url

The base URL on which the web server is serving.

dataset_uid

The ID for this dataset.

obj_i

The index of this data object within the dataset.

local_dir_path

The path to the local directory.

local_dir_uid

A unique identifier for this local directory in this dataset.

Returns

A string for the URL.

Method get_local_file_url()

Construct a URL to a local file.

Usage

AbstractWrapper$get_local_file_url(
  base_url,
  dataset_uid,
  obj_i,
  local_file_path,
  local_file_uid
)

Arguments

base_url

The base URL on which the web server is serving.

dataset_uid

The ID for this dataset.

obj_i

The index of this data object within the dataset.

local_file_path

The path to the local file.

local_file_uid

A unique identifier for this local file in this dataset.

Returns

A string for the URL.

Method get_local_dir_route()

Create a web server route for this object.

Usage

AbstractWrapper$get_local_dir_route(
  dataset_uid,
  obj_i,
  local_dir_path,
  local_dir_uid
)

Arguments

dataset_uid

The ID for this dataset.

obj_i

The index of this data object within the dataset.

local_dir_path

The path to the local directory.

local_dir_uid

A unique identifier for this local directory in this dataset.

Returns

A new VitessceConfigServerStaticRoute instance.

Method get_local_file_route()

Create a web server route for this object.

Usage

AbstractWrapper$get_local_file_route(
  dataset_uid,
  obj_i,
  local_file_path,
  local_file_uid
)

Arguments

dataset_uid

The ID for this dataset.

obj_i

The index of this data object within the dataset.

local_file_path

The path to the local file.

local_file_uid

A unique identifier for this local file in this dataset.

Returns

A new VitessceConfigServerFileRoute instance.

Method get_url()

Create a local web server URL for a dataset object.

Usage

AbstractWrapper$get_url(base_url, dataset_uid, obj_i, ...)

Arguments

base_url

The base URL on which the web server is serving.

dataset_uid

The ID for this dataset.

obj_i

The index of this data object within the dataset.

...

Passes extra arguments to get_route_str

Returns

A URL as a string.

Method get_url_simple()

Construct a URL.

Usage

AbstractWrapper$get_url_simple(base_url, suffix)

Arguments

base_url

The base URL on which the web server is serving.

suffix

The suffix to append to the base URL.

Returns

A URL as a string like base_url/suffix

Method get_route_str()

Create a string representing a web server route path (the part following the base URL).

Usage

AbstractWrapper$get_route_str(dataset_uid, obj_i, ...)

Arguments

dataset_uid

The ID for this dataset.

obj_i

The index of this data object within the dataset.

...

Pastes extra arguments together after obj_i, separated by slash.

Returns

A path as a string.

Method get_out_dir()

Create a directory path to a dataset within the base output directory.

Usage

AbstractWrapper$get_out_dir(dataset_uid, obj_i, ...)

Arguments

dataset_uid

The ID for this dataset.

obj_i

The index of this data object within the dataset.

...

Passes extra arguments to file.path

Returns

A path as a string.

Method auto_view_config()

Automatically configure views for a particular dataset.

Usage

AbstractWrapper$auto_view_config(vc)

Arguments

vc

A VitessceConfig instance to configure.

Method clone()

The objects of this class are cloneable with this method.

Usage

AbstractWrapper$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.