Further work on tasks.

R/DataPreProcessing.R

@@ -293,19 +293,19 @@ determine_preprocessing_parameters <- function(
 
 
 
-.get_feature_info_list <- function(run) {
-
-  # Find pre-processing control element for the current run
-  pre_proc_id_list <- .get_preprocessing_iteration_identifiers(run = run)
-
-  # Load feature info list from backend
-  feature_info_list <- get_feature_info_from_backend(
-    data_id = pre_proc_id_list$data,
-    run_id = pre_proc_id_list$run
-  )
-
-  return(feature_info_list)
-}
+# .get_feature_info_list <- function(run) {
+#   
+#   # Find pre-processing control element for the current run
+#   pre_proc_id_list <- .get_preprocessing_iteration_identifiers(run = run)
+#   
+#   # Load feature info list from backend
+#   feature_info_list <- get_feature_info_from_backend(
+#     data_id = pre_proc_id_list$data,
+#     run_id = pre_proc_id_list$run
+#   )
+#   
+#   return(feature_info_list)
+# }
 
 
 

R/FamiliarS4Generics.R

@@ -377,3 +377,5 @@ setGeneric(".file_exists", function(object, ...) standardGeneric(".file_exists")
 setGeneric(".perform_task", function(object, data, ...) standardGeneric(".perform_task"))
 
 setGeneric(".get_task_descriptor", function(object, ...) standardGeneric(".get_task_descriptor"))
+
+setGeneric(".get_feature_info_list", function(object, ...) standardGeneric(".get_feature_info_list"))

R/TaskFeatureInfo.R

@@ -23,12 +23,10 @@ setMethod(
     if (is.null(file_paths)) return(object)
 
     # Generate file name of pre-processing file
-    file_name <- paste0(object@project_id, "_generic_feature_info.RDS")
-
-    # Add file path and normalise according to the OS
-    object@file <- normalizePath(
-      file.path(file_paths$process_data_dir, file_name),
-      mustWork = FALSE
+    object@file <- get_object_file_name(
+      object_type = "genericFeatureInfo",
+      project_id = object@project_id,
+      dir_path = file_paths$process_data_dir
     )
 
     return(object)
@@ -58,25 +56,23 @@ setMethod(
   function(
     object,
     data,
-    settings = NULL,
+    outcome_info = NULL,
     ...
   ) {
     # This method is called when "data" is expected to be available somewhere in
     # the backend.
-
-    if (is.null(project_info)) {
-      ..error_reached_unreachable_code("project_info is required for retrieving data from the backend.")
-    }
-    if (is.null(settings)) {
-      ..error_reached_unreachable_code("settings is required for retrieving data from the backend.")
+
+    if (is.null(outcome_info)) {
+      ..error_reached_unreachable_code("outcome_info is required.")
     }
 
     # Create a dataObject.
     data <- methods::new(
       "dataObject",
       data = get_data_from_backend(),
       preprocessing_level = "none",
-      outcome_type = settings$data$outcome_type
+      outcome_type = outcome_info@outcome_type,
+      outcome_info = outcome_info
     )
 
     # Pass to .perform_task for dataObject.
@@ -141,15 +137,13 @@ setMethod(
   function(object, file_paths = NULL) {
     if (is.null(file_paths)) return(object)
 
-    # Generate file name of pre-processing file.
-    file_name <- paste0(
-      object@project_id, "_", object@data_id, "_", object@run_id, "_feature_info.RDS"
-    )
-
-    # Add file path and normalise according to the OS
-    object@file <- normalizePath(
-      file.path(file_paths$process_data_dir, file_name),
-      mustWork = FALSE
+    # Generate file name of pre-processing file
+    object@file <- get_object_file_name(
+      object_type = "featureInfo",
+      project_id = object@project_id,
+      data_id = object@data_id,
+      run_id = object@run_id,
+      dir_path = file_paths$process_data_dir
     )
 
     return(object)
@@ -179,8 +173,8 @@ setMethod(
   function(
     object,
     data,
-    settings = NULL,
     project_info = NULL,
+    outcome_info = NULL,
     ...
   ) {
     # This method is called when "data" is expected to be available somewhere in
@@ -189,8 +183,8 @@ setMethod(
     if (is.null(project_info)) {
       ..error_reached_unreachable_code("project_info is required for retrieving data from the backend.")
     }
-    if (is.null(settings)) {
-      ..error_reached_unreachable_code("settings is required for retrieving data from the backend.")
+    if (is.null(outcome_info)) {
+      ..error_reached_unreachable_code("outcome_info is required.")
     }
 
     # Find the run list.
@@ -212,14 +206,14 @@ setMethod(
       "dataObject",
       data = get_data_from_backend(sample_identifiers = sample_identifiers),
       preprocessing_level = "none",
-      outcome_type = settings$data$outcome_type
+      outcome_type = outcome_info@outcome_type,
+      outcome_info = outcome_info
     )
 
     # Pass to method that dispatches with dataObject for further processing.
     return(.perform_task(
       object = object,
       data = data,
-      settings = settings,
       ...
     ))
   }

R/TaskMain.R

@@ -15,6 +15,7 @@ setMethod(
 )
 
 
+
 .generate_trainer_tasks <- function(
     file_paths,
     project_id  
@@ -48,7 +49,7 @@ setMethod(
   # Add tasks related to data processing for learners.
   task_list <- c(
     task_list, 
-    .generate_learner_tasks(
+    .generate_learner_data_preprocessing_tasks(
       file_paths = file_paths,
       project_id = project_id
     )
@@ -58,46 +59,7 @@ setMethod(
 }
 
 
-.generate_vimp_tasks <- function(
-    file_paths,
-    project_id
-) {
-
-  task_list <- list()
-
-  # Check if vimp should be computed separately or is computed during 
-  # hyperparameter optimisation.
-
-  for (data_id in data_ids) {
-    for (run_id in run_ids) {
-      for (vimp_method in vimp_methods) {
-
-        # Check if the variable importance method requires any computation.
-        # For example, signature_only, none and random do not require
-        # computation.
-
-        # Set up variable importance computation task.
-
-        # Set up variable importance hyperparameter task.
-
-      }
-    }
-  }
-
-  # Check if any vimp-related tasks are required.
-  if (len(task_list) == 0L) return(NULL)
-
-  # Add tasks related to data processing for vimp methods.
-  task_list <- c(
-    task_list, 
-    .generate_vimp_data_preprocessing_tasks(
-      file_paths = file_paths,
-      project_id = project_id
-    )
-  )
-
-  return(task_list)
-}
+