Add share argument back to reading functions

R/as_OpenSpecy.R

@@ -147,7 +147,14 @@ as_OpenSpecy <- function(x, ...) {
 #' @rdname as_OpenSpecy
 #'
 #' @export
-as_OpenSpecy.OpenSpecy <- function(x, ...) {
+as_OpenSpecy.OpenSpecy <- function(x, session_id = FALSE, ...) {
+  if(session_id)
+    x$metadata$session_id <- paste(digest(Sys.info()),
+                                   digest(sessionInfo()),
+                                   sep = "/")
+  if(!c("file_id") %in% names(x$metadata))
+    x$metadata$file_id = digest(x[c("wavenumber", "spectra")])
+
   return(x)
 }
 
@@ -246,7 +253,7 @@ as_OpenSpecy.default <- function(x, spectra,
                                    other_info = NULL,
                                    license = "CC BY-NC"),
                                  coords = "gen_grid",
-                                 session_id = F,
+                                 session_id = FALSE,
                                  ...) {
   if (!is.numeric(x) && !is.complex(x) && !is.vector(x))
     stop("'x' must be numeric vector", call. = F)
@@ -281,14 +288,12 @@ as_OpenSpecy.default <- function(x, spectra,
   if (!is.null(metadata)) {
     if (inherits(metadata, c("data.frame", "list"))) {
       obj$metadata <- cbind(obj$metadata, as.data.table(metadata))
-      if(session_id){
+      if(session_id)
         obj$metadata$session_id <- paste(digest(Sys.info()),
                                          digest(sessionInfo()),
                                          sep = "/")
-      }
-      if(!c("file_id") %in% names(obj$metadata)) {
+      if(!c("file_id") %in% names(obj$metadata))
         obj$metadata$file_id = digest(obj[c("wavenumber", "spectra")])
-      }
     } else {
       stop("inconsistent input for 'metadata'", call. = F)
     }

R/read_envi.R

@@ -73,7 +73,8 @@ read_envi <- function(file, header = NULL, share = NULL,
   os <- as_OpenSpecy(x = hdr$wavelength,
                      spectra = dcast(dt, z ~ x + y)[, -1],
                      metadata = c(metadata, md),
-                     coords = dt[, 1:2] |> unique())
+                     coords = dt[, 1:2] |> unique(),
+                     session_id = T)
 
   if (!is.null(share)) share_spec(os, file = file, share = share)
 

R/read_ext.R

@@ -155,7 +155,8 @@ read_text <- function(file, colnames = NULL, method = "fread",
                                               "alternative read method",
                                               call. = F)
 
-  os <- as_OpenSpecy(dt, colnames = colnames, metadata = metadata)
+  os <- as_OpenSpecy(dt, colnames = colnames, metadata = metadata,
+                     session_id = T)
 
   if (!is.null(share)) share_spec(os, file = file, share = share)
 
@@ -204,7 +205,8 @@ read_asp <- function(file, share = NULL,
   y <- lns[-c(1:6)]
   x <- seq(lns[2], lns[3], length.out = lns[1])
 
-  os <- as_OpenSpecy(x, data.table(intensity = y), metadata = metadata)
+  os <- as_OpenSpecy(x, data.table(intensity = y), metadata = metadata,
+                     session_id = T)
 
   if (!is.null(share)) share_spec(os, file = file, share = share)
 
@@ -276,7 +278,8 @@ read_spa <- function(file, share = NULL,
   x <- seq(spr[1], spr[2], length = length(floatData))
   y <- floatData
 
-  os <- as_OpenSpecy(x, data.table(intensity = y), metadata = metadata)
+  os <- as_OpenSpecy(x, data.table(intensity = y), metadata = metadata,
+                     session_id = T)
 
   if (!is.null(share)) share_spec(os, file = file, share = share)
 
@@ -321,16 +324,17 @@ read_jdx <- function(file, share = NULL,
   x <- jdx@wavelength
   y <- as.numeric(unname(jdx@data$spc[1,]))
 
-  file <- readLines(file)
-  test <- file[grepl("##",file)|grepl("[:alpha:]",file)]
-  values <- ifelse(grepl("##",test), gsub("##.{1,}=", "", test),
+  lns <- readLines(file)
+  test <- lns[grepl("##", lns)|grepl("[:alpha:]", lns)]
+  vals <- ifelse(grepl("##",test), gsub("##.{1,}=", "", test),
                    gsub(".{1,}:", "", test))
   names <- ifelse(grepl("##",test), gsub("##", "", gsub("=.{1,}", "", test)),
                   gsub(":.{1,}", "", test))
-  df_metadata <- as.data.table(t(values))
+  df_metadata <- as.data.table(t(vals))
   colnames(df_metadata) <- names
 
-  os <- as_OpenSpecy(x, data.table(intensity = y), metadata = df_metadata)
+  os <- as_OpenSpecy(x, data.table(intensity = y), metadata = df_metadata,
+                     session_id = T)
 
   if (!is.null(share)) share_spec(os, file = file, share = share)
 
@@ -375,7 +379,8 @@ read_spc <- function(file, share = NULL,
   x <- spc@wavelength
   y <- as.numeric(unname(spc@data$spc[1,]))
 
-  os <- as_OpenSpecy(x, data.table(intensity = y), metadata = metadata)
+  os <- as_OpenSpecy(x, data.table(intensity = y), metadata = metadata,
+                     session_id = T)
 
   if (!is.null(share)) share_spec(os, file = file, share = share)
 

R/read_opus.R

@@ -171,7 +171,8 @@ read_opus <- function(file, share = NULL,
 
   os <- as_OpenSpecy(x = res$wavenumbers,
                      spectra = res$spec,
-                     metadata = cbind(as.data.table(metadata), res$metadata))
+                     metadata = cbind(as.data.table(metadata), res$metadata),
+                     session_id = T)
 
   if (!is.null(share)) share_spec(os, file = file, share = share)
 

R/share_spec.R

@@ -63,16 +63,20 @@ share_spec.default <- function(x, ...) {
 share_spec.OpenSpecy <- function(x, file = NULL, share = "system",
                                  credentials = NULL, ...) {
   md <- x$metadata
-  if (any(!c("user_name", "spectrum_type", "spectrum_identity") %in%
-          names(md)) |
-      is.null(md$user_name) | is.null(md$spectrum_type) |
-      is.null(md$spectrum_identity))
+  if(any(!c("user_name", "spectrum_type", "spectrum_identity") %in%
+         names(md)) |
+     is.null(md$user_name) | is.null(md$spectrum_type) |
+     is.null(md$spectrum_identity))
     warning("Fields 'user_name', 'spectrum_type', and 'spectrum_identity' ",
             "should not be empty if you like to share your metadata", call. = F)
 
+  if(is.null(md$session_id))
+    stop("'session_id' must not be empty if you like to share your metadata;",
+         "run 'as_OpenSpecy(x, session_id = T)' to add one", call. = F)
+
   if (share == "system") {
     fp <- file.path(system.file("extdata", package = "OpenSpecy"),
-                    "user_spectra", md$session_id)
+                    "user_spectra", md$session_id) |> unique()
   } else if (share == "cloud") {
     pkg <- "aws.s3"
     mpkg <- pkg[!(pkg %in% installed.packages()[ , "Package"])]
@@ -87,13 +91,13 @@ share_spec.OpenSpecy <- function(x, file = NULL, share = "system",
       stop("'credentials' needs to be a named list containing the following ",
            "items: 's3_key', 's3_secret', 's3_region', 's3_bucket'", call. = F)
 
-    fp <- file.path(tempdir(), md$session_id)
+    fp <- file.path(tempdir(), md$session_id) |> unique()
   } else {
-    fp <- file.path(share, md$session_id)
+    fp <- file.path(share, md$session_id) |> unique()
   }
   dir.create(fp, recursive = T, showWarnings = F)
 
-  fd <- file.path(fp, paste0(md$file_id, ".yml"))
+  fd <- file.path(fp, paste0(md$file_id, ".yml")) |> unique()
 
   write_spec(x, fd)
 

tests/testthat/test-io_spec.R

@@ -25,12 +25,16 @@ test_that("write_spec() works without errors", {
 })
 
 test_that("read_spec() gives expected output", {
-  yml <- read_spec(read_extdata("raman_hdpe.yml")) |> expect_silent()
-  jsn <- read_spec(read_extdata("raman_hdpe.json")) |> expect_silent()
-  rds <- read_spec(read_extdata("raman_hdpe.rds")) |> expect_silent()
+  yml <- read_extdata("raman_hdpe.yml") |> read_spec() |> expect_silent()
+  jsn <- read_extdata("raman_hdpe.json") |> read_spec() |> expect_silent()
+  rds <- read_extdata("raman_hdpe.rds") |> read_spec() |> expect_silent()
 
   read_spec(read_extdata("raman_hdpe.csv")) |> expect_error()
 
+  read_extdata("raman_hdpe.yml") |> read_spec(share = tmp) |> expect_message()
+  read_extdata("raman_hdpe.json") |> read_spec(share = tmp) |> expect_message()
+  read_extdata("raman_hdpe.rds") |> read_spec(share = tmp) |> expect_message()
+
   expect_s3_class(yml, "OpenSpecy")
   expect_s3_class(jsn, "OpenSpecy")
   expect_s3_class(rds, "OpenSpecy")

tests/testthat/test-read_envi.R

@@ -1,6 +1,13 @@
+# Create temp dir for testthat
+tmp <- file.path(tempdir(), "OpenSpecy-testthat")
+dir.create(tmp, showWarnings = F)
+
 test_that("ENVI files are read", {
   tiny_map <- read_extdata("CA_tiny_map.zip") |> read_zip() |>
     expect_silent()
+  read_extdata("CA_tiny_map.zip") |> read_zip(share = tmp) |>
+    expect_message() |> expect_warning()
+
   expect_s3_class(tiny_map, "OpenSpecy")
 
   expect_equal(ncol(tiny_map$spectra), 208)
@@ -17,3 +24,6 @@ test_that("ENVI files are read", {
     expect_contains(c("x", "y", "file_name", "file_id", "description",
                       "pixel size"))
 })
+
+# Tidy up
+unlink(tmp, recursive = T)

tests/testthat/test-read_ext.R

@@ -19,9 +19,9 @@ test_that("extdata files are present", {
 test_that("read_text() gives expected output", {
   csv <- read_extdata("raman_hdpe.csv") |> read_text() |>
     expect_silent()
-  # expect_warning(
-  #   expect_message(read_text(read_extdata("raman_hdpe.csv"), share = tmp))
-  # )
+  read_extdata("raman_hdpe.csv") |> read_text(share = tmp) |>
+    expect_message() |> expect_warning()
+
   dtf <- read_extdata("raman_hdpe.csv") |> read_text(method = "fread") |>
     expect_silent()
   read_extdata("ftir_pva_without_header.csv") |> read_text() |>
@@ -43,6 +43,8 @@ test_that("read_asp() gives expected output", {
     expect_silent()
   read_extdata("raman_hdpe.csv") |> read_asp() |>
     expect_error()
+  read_extdata("ftir_ldpe_soil.asp") |> read_asp(share = tmp) |>
+    expect_message() |> expect_warning()
 
   expect_s3_class(asp, "OpenSpecy")
   expect_equal(names(asp), c("wavenumber", "spectra", "metadata"))
@@ -58,6 +60,9 @@ test_that("read_spa() gives expected output", {
     read_spa() |> expect_silent()
   read_extdata("raman_hdpe.csv") |> read_spa() |>
     expect_error()
+  read_extdata("ftir_polyethylene_reflectance_adjustment_not_working.spa") |>
+    read_spa(share = tmp) |>
+    expect_message() |> expect_warning()
 
   expect_s3_class(spa, "OpenSpecy")
   expect_equal(names(spa), c("wavenumber", "spectra", "metadata"))
@@ -92,6 +97,8 @@ test_that("read_spc() gives expected output", {
     expect_silent()
   read_extdata("raman_hdpe.csv") |> read_spc() |>
     expect_error()
+  read_extdata("raman_atacamit.spc") |> read_spc(share = tmp) |>
+    expect_message() |> expect_warning()
 
   expect_s3_class(spc, "OpenSpecy")
   expect_equal(names(spc), c("wavenumber", "spectra", "metadata"))

tests/testthat/test-read_multi.R

@@ -1,11 +1,22 @@
+# Create temp dir for testthat
+tmp <- file.path(tempdir(), "OpenSpecy-testthat")
+dir.create(tmp, showWarnings = F)
+
 data("raman_hdpe")
 
 test_that("reading in multi files doesn't throw error", {
   expect_silent(multi <- read_extdata("testdata_zipped.zip") |> read_any())
   expect_s3_class(multi, "OpenSpecy")
 
+  read_extdata("testdata_zipped.zip") |> read_any(share = tmp) |>
+    expect_message() |> expect_message() |> expect_message() |>
+    expect_warning() |> expect_warning() |> expect_warning()
+
   expect_equal(multi$wavenumber, raman_hdpe$wavenumber)
   expect_equal(multi$spectra$intensity, raman_hdpe$spectra$intensity)
   expect_equal(multi$spectra$intensity.1, raman_hdpe$spectra$intensity)
   expect_equal(multi$spectra$intensity.2, raman_hdpe$spectra$intensity)
 })
+
+# Tidy up
+unlink(tmp, recursive = T)

tests/testthat/test-read_opus.R

@@ -1,10 +1,16 @@
+# Create temp dir for testthat
+tmp <- file.path(tempdir(), "OpenSpecy-testthat")
+dir.create(tmp, showWarnings = F)
+
 test_that("opus files are read correctly", {
   single <- read_extdata("ftir_ps.0") |> read_opus() |>
     expect_silent()
   multi <- c(read_extdata("ftir_ps.0"), read_extdata("ftir_ps.0")) |>
     read_opus() |> expect_silent()
   read_extdata("raman_hdpe.csv") |> read_opus() |>
     expect_error()
+  read_extdata("ftir_ps.0") |> read_opus(share = tmp) |> expect_message() |>
+    expect_warning()
 
   expect_s3_class(single, "OpenSpecy")
   expect_s3_class(multi, "OpenSpecy")
@@ -29,3 +35,6 @@ test_that("opus files are read correctly", {
                       "hum_abs_sm", "hum_abs_rf", "file_id"))
   expect_identical(names(multi$metadata), names(single$metadata))
 })
+
+# Tidy up
+unlink(tmp, recursive = T)

tests/testthat/test-share_spec.R

@@ -1,15 +1,19 @@
-data("raman_hdpe")
-
 # Create temp dir for testthat
 tmp <- file.path(tempdir(), "OpenSpecy-testthat")
 dir.create(tmp, showWarnings = F)
 
+data("raman_hdpe")
+
 wo_meta <- raman_hdpe
 wo_meta$metadata$spectrum_identity <- NULL
 
 test_that("share_text() gives expected output", {
-  share_spec(raman_hdpe, share = tmp) |>
+  share_spec(raman_hdpe, file = read_extdata("raman_hdpe.csv"), share = tmp) |>
     expect_message()
+  read_extdata("testdata_zipped.zip") |> read_zip() |>
+    share_spec(share = tmp) |>
+    expect_message() |> expect_warning()
+
   file.path(tmp, raman_hdpe$metadata$session_id,
             paste0(raman_hdpe$metadata$file_id, ".yml")) |>
     file.exists() |>