Refactor

DESCRIPTION

@@ -29,6 +29,7 @@ Imports:
     shinyjs,
     stats,
     teal.logger (>= 0.1.1),
+    teal.code,
     utils,
     yaml
 Suggests:

NAMESPACE

@@ -12,6 +12,8 @@ S3method(get_code,default)
 S3method(get_dataname,TealDataAbstract)
 S3method(get_dataname,TealDataset)
 S3method(get_dataname,TealDatasetConnector)
+S3method(get_dataname,ddl)
+S3method(get_dataname,tdata)
 S3method(get_dataset,TealDataAbstract)
 S3method(get_dataset,TealDataset)
 S3method(get_dataset,TealDatasetConnector)
@@ -20,6 +22,10 @@ S3method(get_dataset_label,TealDatasetConnector)
 S3method(get_datasets,TealDataAbstract)
 S3method(get_datasets,TealDataset)
 S3method(get_datasets,TealDatasetConnector)
+S3method(get_datasets,tdata)
+S3method(get_join_keys,TealData)
+S3method(get_join_keys,ddl)
+S3method(get_join_keys,tdata)
 S3method(get_key_duplicates,TealDataset)
 S3method(get_key_duplicates,data.frame)
 S3method(get_keys,TealDataAbstract)
@@ -55,6 +61,7 @@ S3method(to_relational_data,TealDataset)
 S3method(to_relational_data,TealDatasetConnector)
 S3method(to_relational_data,data.frame)
 S3method(to_relational_data,list)
+S3method(to_relational_data,tdata)
 export("col_labels<-")
 export("data_label<-")
 export(as_cdisc)
@@ -79,6 +86,8 @@ export(dataset)
 export(dataset_connector)
 export(dataset_connector_file)
 export(dataset_file)
+export(ddl)
+export(ddl_run)
 export(example_cdisc_data)
 export(fun_cdisc_dataset_connector)
 export(fun_dataset_connector)
@@ -89,11 +98,11 @@ export(get_dataname)
 export(get_dataset)
 export(get_dataset_label)
 export(get_datasets)
+export(get_join_keys)
 export(get_key_duplicates)
 export(get_keys)
 export(get_labels)
 export(get_raw_data)
-export(is_pulled)
 export(join_key)
 export(join_keys)
 export(load_dataset)
@@ -102,6 +111,7 @@ export(mae_dataset)
 export(mutate_data)
 export(mutate_dataset)
 export(mutate_join_keys)
+export(new_tdata)
 export(python_cdisc_dataset_connector)
 export(python_code)
 export(python_dataset_connector)
@@ -113,11 +123,16 @@ export(script_cdisc_dataset_connector)
 export(script_dataset_connector)
 export(set_args)
 export(set_keys)
+export(submit_button_server)
+export(submit_button_ui)
 export(teal_data)
 export(teal_data_file)
 export(to_relational_data)
 export(validate_metadata)
+exportClasses(tdata)
+exportMethods(new_tdata)
 import(shiny)
+import(teal.code)
 importFrom(digest,digest)
 importFrom(logger,log_trace)
 importFrom(shinyjs,show)

R/cdisc_data.R

@@ -68,58 +68,73 @@ cdisc_data <- function(...,
                        code = "",
                        check = FALSE) {
   data_objects <- list(...)
-  checkmate::assert_list(
-    data_objects,
-    types = c("TealDataset", "TealDatasetConnector", "TealDataConnector")
-  )
+
+  # todo: is it really important? - to remove
   if (inherits(join_keys, "JoinKeySet")) {
     join_keys <- teal.data::join_keys(join_keys)
   }
 
-  update_join_keys_to_primary(data_objects, join_keys)
+  if (
+    checkmate::test_list(data_objects, types = c("TealDataConnector", "TealDataset", "TealDatasetConnector"))
+  ) {
+    warning("Using TealDatasetConnector and TealDataset is deprecated, please just include data directly.")
 
-  retrieve_parents <- function(x) {
-    tryCatch(
-      x$get_parent(),
-      error = function(cond) rep(character(0), length(x$get_datanames()))
-    )
-  }
+    update_join_keys_to_primary(data_objects, join_keys)
+
+    retrieve_parents <- function(x) {
+      tryCatch(
+        x$get_parent(),
+        error = function(cond) rep(character(0), length(x$get_datanames()))
+      )
+    }
 
-  new_parents_fun <- function(data_objects) {
-    lapply(data_objects, function(x) {
+    new_parents_fun <- function(data_objects) {
+      lapply(data_objects, function(x) {
+        if (inherits(x, "TealDataConnector")) {
+          unlist(new_parents_fun(x$get_items()), recursive = FALSE)
+        } else {
+          list(retrieve_parents(x))
+        }
+      })
+    }
+
+    new_parents <- unlist(new_parents_fun(data_objects), recursive = FALSE)
+
+    names(new_parents) <- unlist(lapply(data_objects, function(x) {
       if (inherits(x, "TealDataConnector")) {
-        unlist(new_parents_fun(x$get_items()), recursive = FALSE)
+        lapply(x$get_items(), function(z) z$get_dataname())
       } else {
-        list(retrieve_parents(x))
+        x$get_datanames()
       }
-    })
-  }
+    }))
 
-  new_parents <- unlist(new_parents_fun(data_objects), recursive = FALSE)
-
-  names(new_parents) <- unlist(lapply(data_objects, function(x) {
-    if (inherits(x, "TealDataConnector")) {
-      lapply(x$get_items(), function(z) z$get_dataname())
-    } else {
-      x$get_datanames()
+    if (is_dag(new_parents)) {
+      stop("Cycle detected in a parent and child dataset graph.")
     }
-  }))
+    join_keys$set_parents(new_parents)
+    join_keys$update_keys_given_parents()
 
-  if (is_dag(new_parents)) {
-    stop("Cycle detected in a parent and child dataset graph.")
-  }
-  join_keys$set_parents(new_parents)
-  join_keys$update_keys_given_parents()
+    x <- TealData$new(..., check = check, join_keys = join_keys)
+
+    if (length(code) > 0 && !identical(code, "")) {
+      x$set_pull_code(code = code)
+    }
 
-  x <- TealData$new(..., check = check, join_keys = join_keys)
+    x$check_reproducibility()
+    x$check_metadata()
 
-  if (length(code) > 0 && !identical(code, "")) {
-    x$set_pull_code(code = code)
+    if (is_pulled(x)) {
+      new_tdata(
+        env = lapply(x$get_datasets(), function(x) x$get_raw_data()),
+        code = x$get_code(),
+        keys = x$get_join_keys()
+      )
+    } else {
+      x
+    }
+  } else {
+    new_tdata(env = data_objects, code = code, keys = join_keys)
   }
-
-  x$check_reproducibility()
-  x$check_metadata()
-  return(x)
 }
 
 #' Load `TealData` object from a file