WIP: POC Redesign extraction

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9007
+    rev: v0.4.3.9009
     hooks:
       - id: style-files
         name: Style code with `styler`

DESCRIPTION

@@ -31,6 +31,7 @@ Imports:
     shinyjs,
     shinyvalidate (>= 0.1.3),
     stats,
+    teal.code (>= 0.6.0),
     teal.data (>= 0.7.0),
     teal.logger (>= 0.3.1),
     teal.widgets (>= 0.4.3),

NAMESPACE

@@ -1,12 +1,29 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(anyNA,type)
+S3method(c,specification)
+S3method(c,type)
 S3method(data_extract_multiple_srv,FilteredData)
 S3method(data_extract_multiple_srv,list)
 S3method(data_extract_multiple_srv,reactive)
 S3method(data_extract_srv,FilteredData)
 S3method(data_extract_srv,list)
+S3method(determine,colData)
+S3method(determine,datasets)
+S3method(determine,default)
+S3method(determine,list)
+S3method(determine,specification)
+S3method(determine,values)
+S3method(determine,variables)
+S3method(extract,default)
+S3method(extract,teal_data)
 S3method(filter_spec_internal,default)
 S3method(filter_spec_internal,delayed_data)
+S3method(is.delayed,default)
+S3method(is.delayed,list)
+S3method(is.delayed,specification)
+S3method(is.delayed,type)
+S3method(is.na,type)
 S3method(merge_expression_module,list)
 S3method(merge_expression_module,reactive)
 S3method(merge_expression_srv,list)
@@ -19,6 +36,7 @@ S3method(print,delayed_select_spec)
 S3method(print,delayed_value_choices)
 S3method(print,delayed_variable_choices)
 S3method(print,filter_spec)
+S3method(print,type)
 S3method(resolve,default)
 S3method(resolve,delayed_choices_selected)
 S3method(resolve,delayed_data_extract_spec)
@@ -45,6 +63,9 @@ export(data_extract_spec)
 export(data_extract_srv)
 export(data_extract_ui)
 export(datanames_input)
+export(datasets)
+export(determine)
+export(extract)
 export(filter_spec)
 export(first_choice)
 export(first_choices)
@@ -55,21 +76,31 @@ export(get_extract_datanames)
 export(get_merge_call)
 export(get_relabel_call)
 export(is.choices_selected)
+export(is.delayed)
 export(is_single_dataset)
 export(last_choice)
 export(last_choices)
 export(list_extract_spec)
+export(mae_colData)
 export(merge_datasets)
 export(merge_expression_module)
 export(merge_expression_srv)
+export(module_input_server)
+export(module_input_ui)
 export(no_selected_as_NULL)
 export(resolve_delayed)
+export(resolver)
 export(select_spec)
 export(select_spec.default)
 export(select_spec.delayed_data)
 export(split_by_sep)
+export(update_spec)
 export(value_choices)
+export(values)
 export(variable_choices)
+export(variables)
 import(shiny)
 importFrom(dplyr,"%>%")
 importFrom(lifecycle,badge)
+importFrom(methods,is)
+importFrom(tidyselect,everything)

R/delayed.R

@@ -0,0 +1,60 @@
+# Only delay if the type or object really needs it and is not already delayed
+delay <- function(x) {
+  if (is.delayed(x)) {
+    attr(x, "delayed") <- TRUE
+  }
+  x
+}
+
+#' Is the specification resolved?
+#'
+#' Check that the specification is resolved against a given data source.
+#' @param specification Object to be evaluated.
+#' @returns A single logical value.
+#' @examples
+#' is.delayed(1)
+#' is.delayed(variables("df", "df"))
+#' is.delayed(variables("df")) # Unknown selection
+#' @export
+is.delayed <- function(specification) {
+  UseMethod("is.delayed")
+}
+
+#' @export
+#' @method is.delayed default
+is.delayed.default <- function(specification) {
+  # FIXME: A warning?
+  FALSE
+}
+
+# Handling a list of transformers e1 | e2
+#' @export
+#' @method is.delayed list
+is.delayed.list <- function(specification) {
+  any(vapply(specification, is.delayed, logical(1L)))
+}
+
+#' @export
+#' @method is.delayed specification
+is.delayed.specification <- function(specification) {
+  any(vapply(specification, is.delayed, logical(1L)))
+}
+
+#' @export
+#' @method is.delayed type
+is.delayed.type <- function(specification) {
+  if (!is.na(specification)) {
+    return(!all(is.character(specification$choices)) || !all(is.character(specification$selected)))
+  }
+  FALSE
+}
+
+resolved <- function(specification, type = is(specification)) {
+  s <- all(is.character(specification$choices)) && all(is.character(specification$selected))
+
+  if (!s && !all(specification$selected %in% specification$choices)) {
+    stop("Selected ", type, " not resolved.")
+  }
+  attr(specification, "delayed") <- NULL
+  specification
+}

R/extract.R

@@ -0,0 +1,80 @@
+#' Internal method to extract data from different objects
+#'
+#' Required to resolve a specification into something usable (by comparing with the existing data).
+#' Required by merging data based on a resolved specification.
+#' @param x Object from which a subset/element is required.
+#' @param variable Name of the element to be extracted.
+#' @param ... Other arguments passed to the specific method.
+#' @export
+#' @examples
+#' extract(iris, "Sepal.Length")
+extract <- function(x, variable, ...) {
+  UseMethod("extract")
+}
+
+
+#' @export
+extract.default <- function(x, variable, ..., drop = FALSE) {
+  if (length(dim(x)) == 2L || length(variable) > 1L) {
+    x[, variable, drop = drop]
+  } else {
+    x[[variable]]
+  }
+}
+
+#' @export
+extract.teal_data <- function(x, variable, ...) {
+  if (length(variable) > 1L) {
+    x[variable]
+  } else {
+    x[[variable]]
+  }
+}
+
+# @export
+# @method extract data.frame
+# extract.data.frame <- function(x, variable) {
+#   # length(variable) == 1L
+#   x[, variable, drop = TRUE]
+# }
+
+# @export
+# extract.qenv <- function(x, variable) {
+#   x[[variable]]
+# }
+
+# Get code to be evaluated & displayed by modules
+extract_srv <- function(id, input, data) {
+  stopifnot(is.null(input$datasets))
+  stopifnot(is.null(input$variables))
+  moduleServer(
+    id,
+    function(input, output, session) {
+      obj <- extract(data, input$datasets)
+      method <- paste0("extract.", class(obj))
+      method <- dynGet(method, ifnotfound = "extract.default", inherits = TRUE)
+      if (identical(method, "extract.default")) {
+        b <- get("extract.default")
+      } else {
+        b <- get(method)
+      }
+      # Extract definition
+      extract_f_def <- call("<-", x = as.name("extract"), value = b)
+      q <- teal.code::eval_code(data, code = extract_f_def)
+
+      # Extraction happening:
+      # FIXME assumes only to variables used
+      output <- call("<-",
+        x = as.name(input$datasets), value =
+          substitute(
+            extract(obj, variables),
+            list(
+              obj = as.name(input$datasets),
+              variables = input$variables
+            )
+          )
+      )
+      q <- teal.code::eval_code(q, code = output)
+    }
+  )
+}