Implement new wrapper classes for feature parity with Python vitessce

Co-authored-by: keller-mark <7525285+keller-mark@users.noreply.github.com>

Author: Copilot

R/wrappers_images.R

@@ -0,0 +1,141 @@
+#' JSON file wrapper class
+#' @title JsonWrapper Class
+#' @docType class
+#' @description
+#' Class representing a JSON file in a Vitessce dataset.
+#'
+#' @rdname JsonWrapper
+#' @export
+JsonWrapper <- R6::R6Class("JsonWrapper",
+  inherit = AbstractWrapper,
+  public = list(
+    #' @field json_path The path to a local JSON file.
+    #' @keywords internal
+    json_path = NULL,
+    #' @field json_url The URL to a remote JSON file.
+    #' @keywords internal
+    json_url = NULL,
+    #' @field local_json_uid The unique identifier for the local JSON file.
+    #' @keywords internal
+    local_json_uid = NULL,
+    #' @field data_type The Vitessce data type for this file.
+    #' @keywords internal
+    data_type = NULL,
+    #' @field options A list of options to pass to the Vitessce file definition.
+    #' @keywords internal
+    options = NULL,
+    #' @field coordination_values A list of coordination values to pass to the Vitessce file definition.
+    #' @keywords internal
+    coordination_values = NULL,
+    #' @field request_init A list of requestInit values to pass to fetch when loading the JSON over HTTP.
+    #' @keywords internal
+    request_init = NULL,
+    #' @description
+    #' Create a wrapper around a JSON file.
+    #' @param json_path The path to a local JSON file.
+    #' @param json_url The URL to a remote JSON file.
+    #' @param data_type The Vitessce data type for this file.
+    #' @param options A list of options to pass to the Vitessce file definition.
+    #' @param coordination_values A list of coordination values to pass to the Vitessce file definition.
+    #' @param request_init A list of requestInit values to pass to fetch when loading the JSON over HTTP.
+    #' @param ... Parameters inherited from `AbstractWrapper`.
+    #' @return A new `JsonWrapper` object.
+    initialize = function(json_path = NA, json_url = NA, data_type = NA, options = NA, coordination_values = NA, request_init = NA, ...) {
+      super$initialize(...)
+      self$json_path <- json_path
+      self$json_url <- json_url
+
+      if(is_na(data_type)) {
+        stop("Expected data_type to be provided.")
+      }
+
+      if(!is.na(json_url) && !is.na(json_path)) {
+        stop("Did not expect json_url to be provided with json_path.")
+      }
+
+      if(is.na(json_url) && is.na(json_path)) {
+        stop("Expected either json_url or json_path to be provided.")
+      }
+
+      if(!is.na(json_path)) {
+        self$is_remote <- FALSE
+      } else {
+        self$is_remote <- TRUE
+      }
+
+      self$local_json_uid <- make_unique_filename(".json")
+
+      self$data_type <- data_type
+      self$options <- options
+      self$coordination_values <- coordination_values
+      self$request_init <- request_init
+    },
+    #' @description
+    #' Create the JSON output files, web server routes, and file definition creators.
+    #' @param dataset_uid The ID for this dataset.
+    #' @param obj_i The index of this data object within the dataset.
+    #' @param base_dir A base directory for local data.
+    convert_and_save = function(dataset_uid, obj_i, base_dir = NA) {
+      if(!self$is_remote) {
+        super$convert_and_save(dataset_uid, obj_i, base_dir = base_dir)
+      }
+
+      # Get the file definition creator functions.
+      file_def_creator <- self$make_file_def_creator(dataset_uid, obj_i)
+
+      # Append the new file definition creators functions to the main list.
+      self$file_def_creators <- append(self$file_def_creators, file_def_creator)
+
+      # Create a web server route object for the directory of JSON files.
+      new_routes <- self$make_routes(dataset_uid, obj_i)
+      for(route in new_routes) {
+        self$routes <- append(self$routes, route)
+      }
+    },
+    #' @description
+    #' Get a list of server route objects.
+    #' @param dataset_uid The ID for this dataset.
+    #' @param obj_i The index of this data object within the dataset.
+    make_routes = function(dataset_uid, obj_i) {
+      return(self$get_local_file_route(dataset_uid, obj_i, self$json_path, self$local_json_uid))
+    },
+    #' @description
+    #' Get the URL to the JSON file, to fill in the file URL in the file definitions.
+    #' @param base_url The base URL, on which the route will be served.
+    #' @param dataset_uid The ID for this dataset.
+    #' @param obj_i The index of this data object within the dataset.
+    #' @keywords internal
+    #' @return A URL as a string.
+    get_json_url = function(base_url, dataset_uid, obj_i) {
+      if(self$is_remote) {
+        return(self$json_url)
+      } else {
+        return(self$get_local_file_url(base_url, dataset_uid, obj_i, self$json_path, self$local_json_uid))
+      }
+    },
+    #' @description
+    #' Make the file definition creator function for the JSON data type.
+    #' @param dataset_uid The ID for this dataset.
+    #' @param obj_i The index of this data object within the dataset.
+    #' @return A file definition creator function which takes a `base_url` parameter.
+    make_file_def_creator = function(dataset_uid, obj_i) {
+      get_json <- function(base_url) {
+        file_def <- list(
+          fileType = paste0(self$data_type, ".json"),
+          url = self$get_json_url(base_url, dataset_uid, obj_i)
+        )
+        if(!is_na(self$options)) {
+          file_def[['options']] <- self$options
+        }
+        if(!is_na(self$request_init)) {
+          file_def[['requestInit']] <- self$request_init
+        }
+        if(!is_na(self$coordination_values)) {
+          file_def[['coordinationValues']] <- self$coordination_values
+        }
+        return(file_def)
+      }
+      return(get_json)
+    }
+  ),
+)