remove hashing (#119)

related to insightsengineering/teal#751

remove datasets hashing and transfer it to `teal`.

Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>

NEWS.md

@@ -2,6 +2,7 @@
 
 * Examples now use `scda.2022` instead of `scda.2021`.
 * Modified `teal.Dataset$print` method for a less cluttered output.
+* Transferred data hashing step in `TealDataset` and `MAETealDataset` to `teal`.
 
 # teal.data 0.1.2
 

R/MAETealDataset.R

@@ -75,7 +75,6 @@ MAETealDataset <- R6::R6Class( # nolint
       self$set_vars(vars)
       self$set_dataset_label(label)
       self$set_keys(keys)
-      private$calculate_hash()
 
       # needed if recreating dataset - we need to preserve code order and uniqueness
       private$code <- CodeClass$new()
@@ -96,7 +95,9 @@ MAETealDataset <- R6::R6Class( # nolint
     #' `TRUE` if the dataset generated from evaluating the
     #' `get_code()` code is identical to the raw data, else `FALSE`.
     check = function() {
-      logger::log_trace("TealDataset$check executing the code to reproduce dataset: { deparse1(self$get_dataname()) }...")
+      logger::log_trace(
+        "TealDataset$check executing the code to reproduce dataset: { deparse1(self$get_dataname()) }..."
+      )
       if (!checkmate::test_character(self$get_code(), len = 1, pattern = "\\w+")) {
         stop(
           sprintf(
@@ -274,7 +275,7 @@ MAETealDataset <- R6::R6Class( # nolint
 #' mae_d$get_code()
 #' mae_d$get_raw_data()
 #' @export
-dataset.MultiAssayExperiment <- function(dataname,
+dataset.MultiAssayExperiment <- function(dataname, # nolint
                                          x,
                                          keys = character(0),
                                          label = data_label(x),

R/TealDataset.R

@@ -73,7 +73,6 @@ TealDataset <- R6::R6Class( # nolint
       self$set_vars(vars)
       self$set_dataset_label(label)
       self$set_keys(keys)
-      private$calculate_hash()
 
       # needed if recreating dataset - we need to preserve code order and uniqueness
       private$code <- CodeClass$new()
@@ -256,12 +255,6 @@ TealDataset <- R6::R6Class( # nolint
       private$join_keys
     },
     #' @description
-    #' Returns the string representation of the raw data hashed with the MD5 hash algorithm.
-    #' @return `character` the hash of the raw data
-    get_hash = function() {
-      private$data_hash
-    },
-    #' @description
     #' Get the list of dependencies that are `TealDataset` or `TealDatasetConnector` objects
     #'
     #' @return `list`
@@ -303,7 +296,9 @@ TealDataset <- R6::R6Class( # nolint
       common_mutate_vars <- intersect(names(datasets), names(private$mutate_vars))
       private$mutate_vars[common_mutate_vars] <- datasets[common_mutate_vars]
 
-      logger::log_trace("TealDataset$reassign_datasets_vars reassigned vars for dataset: { deparse1(self$get_dataname()) }.")
+      logger::log_trace(
+        "TealDataset$reassign_datasets_vars reassigned vars for dataset: { deparse1(self$get_dataname()) }."
+      )
       invisible(NULL)
     },
     #' @description
@@ -316,7 +311,9 @@ TealDataset <- R6::R6Class( # nolint
       checkmate::assert_character(label, max.len = 1, any.missing = FALSE)
       private$dataset_label <- label
 
-      logger::log_trace("TealDataset$set_dataset_label dataset_label set for dataset: { deparse1(self$get_dataname()) }.")
+      logger::log_trace(
+        "TealDataset$set_dataset_label dataset_label set for dataset: { deparse1(self$get_dataname()) }."
+      )
       return(invisible(self))
     },
     #' @description
@@ -360,7 +357,10 @@ TealDataset <- R6::R6Class( # nolint
     mutate_join_keys = function(dataset, val) {
       self$get_join_keys()$mutate(private$dataname, dataset, val)
       logger::log_trace(
-        "TealDatasetConnector$mutate_join_keys join_keys modified keys of { deparse1(self$get_dataname()) } against { dataset }."
+        paste0(
+          "TealDatasetConnector$mutate_join_keys join_keys modified keys",
+          "of { deparse1(self$get_dataname()) } against { dataset }."
+        )
       )
       return(invisible(self))
     },
@@ -523,7 +523,9 @@ TealDataset <- R6::R6Class( # nolint
     #' `TRUE` if the dataset generated from evaluating the
     #' `get_code()` code is identical to the raw data, else `FALSE`.
     check = function() {
-      logger::log_trace("TealDataset$check executing the code to reproduce dataset: { deparse1(self$get_dataname()) }...")
+      logger::log_trace(
+        "TealDataset$check executing the code to reproduce dataset: { deparse1(self$get_dataname()) }..."
+      )
       if (!checkmate::test_character(self$get_code(), len = 1, pattern = "\\w+")) {
         stop(
           sprintf(
@@ -596,7 +598,6 @@ TealDataset <- R6::R6Class( # nolint
     .keys = character(0),
     mutate_code = list(),
     mutate_vars = list(),
-    data_hash = character(0),
     join_keys = NULL,
 
     ## __Private Methods ====
@@ -614,7 +615,9 @@ TealDataset <- R6::R6Class( # nolint
       return(invisible(self))
     },
     mutate_eager = function() {
-      logger::log_trace("TealDatasetConnector$mutate_eager executing mutate code for dataset: { deparse1(self$get_dataname()) }...")
+      logger::log_trace(
+        "TealDatasetConnector$mutate_eager executing mutate code for dataset: { deparse1(self$get_dataname()) }..."
+      )
       new_df <- private$execute_code(
         code = private$mutate_list_to_code_class(),
         vars = c(
@@ -628,7 +631,7 @@ TealDataset <- R6::R6Class( # nolint
 
       # code set after successful evaluation
       # otherwise code != dataset
-      # private$code$append(private$mutate_code)
+      # private$code$append(private$mutate_code) # nolint
       private$append_mutate_code()
       self$set_vars(private$mutate_vars)
       private$mutate_code <- list()
@@ -642,7 +645,9 @@ TealDataset <- R6::R6Class( # nolint
         vars = list()
       )
 
-      logger::log_trace("TealDatasetConnector$mutate_eager executed mutate code for dataset: { deparse1(self$get_dataname()) }.")
+      logger::log_trace(
+        "TealDatasetConnector$mutate_eager executed mutate code for dataset: { deparse1(self$get_dataname()) }."
+      )
 
       new_self
     },
@@ -788,13 +793,6 @@ TealDataset <- R6::R6Class( # nolint
       return(new_set)
     },
 
-    # Calculates the MD5 hash of the raw data stored in this TealDataset.
-    # @return NULL
-    calculate_hash = function() {
-      private$data_hash <- digest::digest(self$get_raw_data(), algo = "md5")
-      NULL
-    },
-
     # Set the name for the dataset
     # @param dataname (`character`) the new name
     # @return self invisibly for chaining

tests/testthat/test-TealData.R

@@ -147,16 +147,6 @@ test_that("deep clone", {
   expect_false(rlang::is_reference(x$get_join_keys(), x_copy$get_join_keys()))
 })
 
-testthat::test_that("The hashes of TealDatasets objects are correct after mutating the TealData object", {
-  mutated_iris <- iris
-  mutated_iris$test <- 1
-  mutated_iris_hash <- digest::digest(mutated_iris, algo = "md5")
-  rd <- teal_data(dataset("iris", iris))
-  mutate_data(rd, code = "iris$test <- 1")
-  rd$execute_mutate()
-  testthat::expect_equal(rd$get_dataset("iris")$get_hash(), mutated_iris_hash)
-})
-
 testthat::test_that("execute_mutate returns current datasets if no mutate_code", {
   pull_fun <- callable_function(data.frame)
   pull_fun$set_args(args = list(head_letters = head(letters)))

tests/testthat/test-TealDataset.R

@@ -445,12 +445,6 @@ testthat::test_that("TealDataset$check returns FALSE if the passed code creates
   testthat::expect_false(test_ds0$check())
 })
 
-testthat::test_that("get_hash returns the hash of the object passed to the constructor", {
-  iris_hash <- digest::digest(iris, algo = "md5")
-  ds <- TealDataset$new("iris", iris)
-  testthat::expect_equal(ds$get_hash(), iris_hash)
-})
-
 testthat::test_that("get_code_class returns the correct CodeClass object", {
   cc1 <- CodeClass$new(code = "iris <- head(iris)", dataname = "iris")
   cc2 <- CodeClass$new(code = "mtcars <- head(mtcars)", dataname = "mtcars", deps = "iris")
@@ -758,14 +752,6 @@ test_that("mutate_dataset with vars argument", {
   )
 })
 
-testthat::test_that("get_hash returns the correct hash after mutating the TealDataset object", {
-  mutated_iris <- iris
-  mutated_iris$test <- 1
-  mutated_iris_hash <- digest::digest(mutated_iris, algo = "md5")
-  ds <- TealDataset$new("iris", iris) %>% mutate_dataset("iris$test <- 1")
-  testthat::expect_equal(ds$get_hash(), mutated_iris_hash)
-})
-
 testthat::test_that("dataset$merge_join_keys does not throw on basic input", {
   dataset1 <- TealDataset$new("iris", head(iris))
   dataset1$set_join_keys(join_key("iris", "other_dataset", c("Species" = "some_col")))