#fixes 211 can import foldered data from downloads

R/importRDBESDataZIP.R

@@ -54,6 +54,24 @@ importRDBESDataZIP <- function(filenames,
 
   # the files are not used currently but can be if we want to
   files <- unique(unlist(sapply(filenames, unzipFile, tmp)))
+
+  dirs <- list.dirs(tmp, full.names = FALSE, recursive = FALSE)
+  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.")
+    }
+    #remove directory structure
+    for(d in dirs){
+      files <- list.files(file.path(tmp, d), full.names = FALSE)
+      file.rename(file.path(tmp, d, files), file.path(tmp, files))
+    }
+
+
+  }
+
   res <- importRDBESDataCSV(tmp,
                             castToCorrectDataTypes = castToCorrectDataTypes)
   unlink(tmp, recursive = T)

data-raw/create_H1_ExampleData.R

@@ -1,13 +1,92 @@
 ## Load the csv files from our data-raw
 ddir <- "./data-raw/exampleData/"
-outputDir <- "./tests/testthat/h1_v_1_19_18/"
+outputDir <- "./tests/testthat/h1_v_1_19_26/"
 
 H1_2023_10_16 <- createRDBESDataObject(paste0(ddir, "H1_2023_10_16.zip"),
                                        castToCorrectDataTypes = TRUE)
 validateRDBESDataObject(H1_2023_10_16)
 
-saveRDS(H1_2023_10_16, file=paste0(outputDir,"H1_2023_10_16.rds"))
+#copy the zip file to tests
+file.copy(paste0(ddir, "H1_2023_10_16.zip"), paste0(outputDir, "H1_2023_10_16.zip"), overwrite = TRUE)
+
+#saveRDS(H1_2023_10_16, file=paste0(outputDir,"H1_2023_10_16.rds"))
+
 
 H1Example <- H1_2023_10_16
 # Save the data
 usethis::use_data(H1Example, overwrite = TRUE)
+
+# make a different zip file according to the changed download format
+
+# Generates random number for the temp import folder name
+randInt <- paste0(sample(1:100, 3), collapse = "")
+tmp <- paste0(tempdir(), "/downloadImport", randInt)
+dir.create(tmp)
+all_unzipped <- c()
+unzipFile <- function(x, tmp) {
+
+  if (!file.exists(x)) {
+    return()
+  }
+
+  if (RDBEScore:::is.zip(x)) {
+    unzipped <- utils::unzip(x, exdir= tmp)
+    unzipped <- basename(unzipped)
+    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")))
+    }
+    all_unzipped <<- c(all_unzipped, unzipped)
+    return(unzipped)
+  }
+
+}
+
+# the files are not used currently but can be if we want to
+files <- unzipFile(paste0(ddir, "H1_2023_10_16.zip"), tmp)
+
+#make folders in tmp
+dir.create(paste0(tmp, "/H1"))
+dir.create(paste0(tmp, "/HVD"))
+dir.create(paste0(tmp, "/HSL"))
+#put files to the folders
+hsl_file <- "SpeciesList.csv"
+hvd_file <- "VesselDetails.csv"
+file.copy(paste0(tmp, "/", hsl_file), paste0(tmp, "/HSL"), overwrite = TRUE)
+file.copy(paste0(tmp, "/", hvd_file), paste0(tmp, "/HVD"), overwrite = TRUE)
+#all others files
+h1_files <- setdiff(files, c(hsl_file, hvd_file))
+for (file in h1_files) {
+  file.copy(paste0(tmp, "/", file), paste0(tmp, "/H1"), overwrite = TRUE)
+}
+#remove all csv files from the tmp folder
+unlink(paste0(tmp, "/", files), recursive = F)
+
+
+
+#zip the temp so it has the same format as the download
+# Zip the 'H1', 'HVD', and 'HSL' folders without including the 'tmp' directory
+zip(paste0(outputDir, "H1_2023_10_16_fd.zip"),
+    files = files_to_zip,  # Relative paths inside tmp
+    flags = "-r",
+    extras = paste0("-j ", tmp))
+
+#define the name and path of the final ZIP file
+final_zip <- paste0(getwd(),file.path(outputDir, "H1_2023_10_16_fd.zip"))
+
+zip::zipr(zipfile = final_zip,
+          files = c("H1", "HVD", "HSL", "Disclaimer.txt"),
+          root = tmp)
+
+#make a new Directory in tmp claled H2 and zip it
+final_zip <- paste0(getwd(),file.path(outputDir, "H1_H2_2023_10_16_fd.zip"))
+dir.create(paste0(tmp, "/H2"))
+zip::zipr(zipfile = final_zip,
+          files = c("H1","H2", "HVD", "HSL", "Disclaimer.txt"),
+          root = tmp)
+
+
+# remove the temp folder
+unlink(tmp, recursive = T)
+

tests/testthat/test-createRDBESDataObject.R

@@ -57,6 +57,31 @@ capture.output({  ## suppresses printing of console output when running test()
 
   # Test ZIP inputs ---------------------------------------------------------
 
+  test_that("importing foldered zipped H1 example data works", {
+    zipFiles <- c(
+      "H1_2023_10_16_fd.zip"
+    )
+
+    genObj <- createRDBESDataObject(paste0(dirH1, zipFiles),
+                                    castToCorrectDataTypes = TRUE)
+
+    expect_equal(genObj, expObjH1)
+
+  })
+
+  test_that("importing foldered zipped H1 and H2 gives an error", {
+    zipFiles <- c(
+      "H1_H2_2023_10_16_fd.zip"
+    )
+
+    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."
+    )
+
+  })
+
   test_that("importing zipped H1 example data works", {
     zipFiles <- c(
       "H1_2023_10_16.zip"