can import from multiple hierarchy zip if hierarchy is set

ices-tools-dev · Nov 5, 2024 · 2dc0129 · 2dc0129
1 parent 78c6a42
commit 2dc0129
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Showing 4 changed files with 56 additions and 9 deletions.
diff --git a/R/createRDBESDataObject.R b/R/createRDBESDataObject.R
@@ -89,7 +89,7 @@ createRDBESDataObject <- function(input = NULL,
   # -------------------------------------------------------------------------
 
   if(import.type == "zip") output <- importRDBESDataZIP(filenames = input,
-                                                        castToCorrectDataTypes = castToCorrectDataTypes)
+                                                        castToCorrectDataTypes = castToCorrectDataTypes, ...)
 
   if(import.type == "csv") output <- importRDBESDataCSV(rdbesExtractPath = input,
                                                            listOfFileNames = listOfFileNames,

diff --git a/R/importRDBESDataZIP.R b/R/importRDBESDataZIP.R
@@ -11,6 +11,8 @@
 #'   attempt to cast the required columns to the correct data type.  If `FALSE`
 #'   then the column data types will be determined by how the csv files are read
 #'   in. Default is `TRUE`.
+#'  @param Hierarchy - Optional. A number specifying the hierarchy of the data
+#'   to be imported. If the .zip file contains multiple hierarchies.
 #'
 #' @return a list of all the RDBES data tables The table that are not in input
 #'   data are NULL
@@ -25,7 +27,8 @@
 #' }
 
 importRDBESDataZIP <- function(filenames,
-                               castToCorrectDataTypes = TRUE) {
+                               castToCorrectDataTypes = TRUE,
+                               Hierarchy = NULL) {
 
   # Generates random number for the temp import folder name
   randInt <- paste0(sample(1:100, 3), collapse = "")
@@ -44,7 +47,8 @@ importRDBESDataZIP <- function(filenames,
       unzipped <- unzipped[grep("*.csv", unzipped)]
       intersected <- intersect(unzipped, all_unzipped)
       if(length(intersected) != 0) {
-        warning(paste0("Duplicate unzipped files detected:\n",  paste0("\t", intersected, "\n", collapse="\n")))
+        warning(paste0("Duplicate unzipped files detected:\n",
+                       paste0("\t", intersected, "\n", collapse="\n")))
       }
       all_unzipped <<- c(all_unzipped, unzipped)
       return(unzipped)
@@ -59,9 +63,23 @@ importRDBESDataZIP <- function(filenames,
   if(length(dirs) > 0) {
     hdirs <- dirs[grepl("H[0-9]+", dirs)]
     if(length(hdirs) > 1) {
-      stop("You cannot import a mix of different hierarchies in one 'zip' ",
-           "input. To import multiple tables unzip all files and import as ",
-           "a folder of 'csv' files.")
+      valid_hierarchies <- as.numeric(gsub("H", "", hdirs))
+      example  <- paste0("Hierachy = ", valid_hierarchies[1])
+      if(is.null(Hierarchy)) {
+        stop("The zip file contains multiple hierarchies.\n",
+             "To import a selected hierarchy, please provide the hierarchy ",
+             "as an argument e.g like:\n",example)
+      }
+      else if(!Hierarchy %in% valid_hierarchies) {
+        stop("The zip file does not contain the hierarchy specified. ",
+             "The options are: ", paste0(valid_hierarchies, collapse = ", "),
+             "\nPlease provide a valid hierarchy as an argument. e.g like:\n",
+             example)
+
+      }
+      else {
+        dirs <- c(setdiff(dirs, hdirs), paste0("H", Hierarchy))
+      }
     }
     #remove directory structure
     for(d in dirs){

diff --git a/man/importRDBESDataZIP.Rd b/man/importRDBESDataZIP.Rd
diff --git a/tests/testthat/test-createRDBESDataObject.R b/tests/testthat/test-createRDBESDataObject.R
@@ -77,7 +77,34 @@ capture.output({  ## suppresses printing of console output when running test()
     genObj <- expect_error(
       createRDBESDataObject(paste0(dirH1, zipFiles),
                             castToCorrectDataTypes = TRUE),
-      "You cannot import a mix of different hierarchies in one 'zip' input. To import multiple tables unzip all files and import as a folder of 'csv' files."
+      "The zip file contains multiple hierarchies.\nTo import a selected hierarchy, please provide the hierarchy as an argument e.g like:\nHierachy = 1"
+    )
+
+  })
+
+  test_that("importing foldered zipped H1 and H2 example data works when hierarchy is specified", {
+    zipFiles <- c(
+      "H1_H2_2023_10_16_fd.zip"
+    )
+
+    genObj <- createRDBESDataObject(paste0(dirH1, zipFiles),
+                                    castToCorrectDataTypes = TRUE,
+                                    Hierarchy = 1)
+
+    expect_equal(genObj, expObjH1)
+
+  })
+
+  test_that("importing foldered zipped H1 and H2 example does not work when hierarchy is misspecified", {
+    zipFiles <- c(
+      "H1_H2_2023_10_16_fd.zip"
+    )
+
+    genObj <- expect_error(
+      createRDBESDataObject(paste0(dirH1, zipFiles),
+                            castToCorrectDataTypes = TRUE,
+                            Hierarchy = "H1"),
+      "The zip file does not contain the hierarchy specified. The options are: 1, 2\nPlease provide a valid hierarchy as an argument. e.g like:\nHierachy = 1"
     )
 
   })