Export nemo metadata

DESCRIPTION

@@ -29,6 +29,7 @@ Imports:
     rlang,
     tibble,
     tidyr,
+    ulid,
     yaml
 Suggests:
     argparse,

NAMESPACE

@@ -18,6 +18,7 @@ export(list_files_dir)
 export(nemo_cli)
 export(nemo_log)
 export(nemo_log_date)
+export(nemo_osfx)
 export(nemo_out_formats)
 export(nemo_write)
 export(nemoverse_wf_dispatch)

R/Tool.R

@@ -5,7 +5,6 @@
 #' @examples
 #' \dontrun{
 #' path <- here::here("inst/extdata/tool1")
-#' x <- Tool$new("tool1", pkg = "nemo", path = path)
 #' # demo filter + tidy
 #' x <- Tool1$new(path = path)$
 #'   filter_files(exclude = "alignments_dupfreq")$
@@ -351,27 +350,34 @@ Tool <- R6::R6Class(
     #' Directory path to output tidy files. Ignored if format is db.
     #' @param format (`character(1)`)\cr
     #' Format of output files.
-    #' @param id (`character(1)`)\cr
-    #' ID to use for the dataset (e.g. `wfrid.123`, `prid.456`).
+    #' @param input_id (`character(1)`)\cr
+    #' Input ID to use for the dataset (e.g. `wfrid.123`, `prid.456`).
     #' @param dbconn (`DBIConnection`)\cr
     #' Database connection object (see `DBI::dbConnect`).
+    #' @param output_id (`character(1)`)\cr
+    #' Output ID to use for the dataset (e.g. `wfrid.123`, `prid.456`).
     #' @return A tibble with the tidy data and their output location prefix.
-    write = function(odir = ".", format = "tsv", id = NULL, dbconn = NULL) {
+    write = function(
+      odir = ".",
+      format = "tsv",
+      input_id = NULL,
+      dbconn = NULL,
+      output_id = ulid::ulid()
+    ) {
       if (format != "db") {
         if (is.null(odir)) {
           stop("Output directory must be specified when format is not 'db'.")
         }
         fs::dir_create(odir)
         odir <- normalizePath(odir)
       }
-      stopifnot(!is.null(id))
+      stopifnot(!is.null(input_id), !is.null(output_id))
       stopifnot("Did you forget to tidy?" = !private$needs_tidying)
       if (is.null(self$tbls)) {
         # even though tidying is not needed, there must be no files detected
         # for tidying (and therefore writing). So return NULL.
         return(NULL)
       }
-
       d_write <- self$tbls |>
         dplyr::select(
           "tool_parser",
@@ -385,8 +391,9 @@ Tool <- R6::R6Class(
           tidy_data = list(
             tidy_data |>
               tibble::add_column(
-                nemo_id = as.character(id),
-                nemo_pfix = as.character(prefix),
+                input_id = as.character(input_id),
+                input_pfix = as.character(prefix),
+                output_id = as.character(output_id),
                 .before = 1
               )
           ),
@@ -411,18 +418,26 @@ Tool <- R6::R6Class(
               dbconn = dbconn,
               dbtab = .data$dbtab
             )
-          )
+          ),
+          outpath = attr(out, "outpath")
         ) |>
-        dplyr::ungroup()
+        dplyr::ungroup() |>
+        dplyr::select(
+          "tool_parser",
+          "prefix",
+          "tidy_data",
+          "tbl_name",
+          "outpath"
+        )
       invisible(d_write)
     },
     #' @description Parse, filter, tidy and write files.
     #' @param odir (`character(1)`)\cr
     #' Directory path to output tidy files.
     #' @param format (`character(1)`)\cr
     #' Format of output files.
-    #' @param id (`character(1)`)\cr
-    #' ID to use for the dataset (e.g. `wfrid.123`, `prid.456`).
+    #' @param input_id (`character(1)`)\cr
+    #' Input ID to use for the dataset (e.g. `wfrid.123`, `prid.456`).
     #' @param dbconn (`DBIConnection`)\cr
     #' Database connection object (see `DBI::dbConnect`).
     #' @param include (`character(n)`)\cr
@@ -433,7 +448,7 @@ Tool <- R6::R6Class(
     nemofy = function(
       odir = ".",
       format = "tsv",
-      id = NULL,
+      input_id = NULL,
       dbconn = NULL,
       include = NULL,
       exclude = NULL
@@ -445,7 +460,7 @@ Tool <- R6::R6Class(
         write(
           odir = odir,
           format = format,
-          id = id,
+          input_id = input_id,
           dbconn = dbconn
       )
     }

R/write.R

@@ -47,23 +47,20 @@ nemo_write <- function(d, fpfix = NULL, format = "tsv", dbconn = NULL, dbtab = N
   } else {
     stopifnot(!is.null(fpfix))
     fpfix <- as.character(fpfix)
-    sfx <- c(tsv = "tsv.gz", csv = "csv.gz", parquet = "parquet", rds = "rds")
-    osfx <- function(s) glue("{fpfix}.{sfx[s]}")
+    osfx <- nemo_osfx(fpfix, format)
     fs::dir_create(dirname(fpfix))
-    if (format == "tsv") {
-      readr::write_tsv(d, osfx("tsv"))
-    } else if (format == "csv") {
-      readr::write_csv(d, osfx("csv"))
-    } else if (format == "parquet") {
-      arrow::write_parquet(d, osfx("parquet"))
-    } else if (format == "rds") {
-      readr::write_rds(d, osfx("rds"))
-    } else {
-      stop("No where else to go, check your output format!")
-    }
+    w <- list(
+      tsv = list(fun = "write_tsv", pkg = "readr"),
+      csv = list(fun = "write_csv", pkg = "readr"),
+      parquet = list(fun = "write_parquet", pkg = "arrow"),
+      rds = list(fun = "write_rds", pkg = "readr")
+    )
+    x <- w[[format]]
+    fun <- getExportedValue(x[["pkg"]], x[["fun"]])
+    fun(d, osfx)
   }
-  # also gets returned in case of NULL format
-  return(invisible(d))
+  attr(d, "outpath") <- if (format == "db") NULL else osfx
+  invisible(d)
 }
 
 #' Output Format is Valid
@@ -93,3 +90,26 @@ valid_out_fmt <- function(x, choices = nemo_out_formats()) {
 nemo_out_formats <- function() {
   c("parquet", "db", "tsv", "csv", "rds")
 }
+
+#' Construct Output File Paths with Format Suffix
+#'
+#' @param fpfix (`character(n)`)\cr
+#' Vector of one or more file prefixes e.g. /path/to/foo
+#' @param format (`character(1)`)\cr
+#' Output format. One of tsv, csv, parquet, rds, or db.
+#' @return Character vector of output file paths
+#'
+#' @examples
+#' fpfix <- "path/to/foo"
+#' format <- "tsv"
+#' o <- nemo_osfx(fpfix, format)
+#' @testexamples
+#' expect_equal(o, glue("{fpfix}.tsv.gz"))
+#'
+#' @export
+nemo_osfx <- function(fpfix, format) {
+  valid_out_fmt(format)
+  fpfix <- as.character(fpfix)
+  sfx <- c(tsv = "tsv.gz", csv = "csv.gz", parquet = "parquet", rds = "rds")
+  paste0(fpfix, ".", sfx[format])
+}

tests/testthat/test-roxytest-testexamples-write.R

@@ -13,11 +13,20 @@ test_that("Function nemo_write() @ L34", {
 })
 
 
-test_that("Function valid_out_fmt() @ L81", {
+test_that("Function valid_out_fmt() @ L77", {
 
   valid_out_fmt("tsv")
   expect_true(valid_out_fmt("tsv"))
   expect_error(valid_out_fmt("foo"))
   expect_error(valid_out_fmt(c("tsv", "csv")))
 })
 
+
+test_that("Function nemo_osfx() @ L109", {
+
+  fpfix <- "path/to/foo"
+  format <- "tsv"
+  o <- nemo_osfx(fpfix, format)
+  expect_equal(o, glue("{fpfix}.tsv.gz"))
+})
+