v1.3.1

.Rbuildignore

@@ -16,6 +16,7 @@
 ^[.]?air[.]toml$
 ^\.vscode$
 ^jarl\.yml$
+^jarl\.toml$
 ^data-raw$
 ^AGENTS.md$
 ^assets$

CITATION.cff

@@ -8,7 +8,7 @@ message: 'To cite package "GeoLocatoR" in publications use:'
 type: software
 license: GPL-3.0-or-later
 title: 'GeoLocatoR: R package for GeoLocator Data Package'
-version: 1.3.0
+version: 1.3.1
 identifiers:
 - type: url
   value: https://geopressure.org/GeoLocatoR/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GeoLocatoR
 Title: R package for GeoLocator Data Package
-Version: 1.3.0
+Version: 1.3.1
 Authors@R: 
     c(
       person("Raphaël", "Nussbaumer", , "rafnuss@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-8185-1020")),

NEWS.md

@@ -1,3 +1,18 @@
+# GeoLocatoR v1.3.1
+
+## Main
+
+- [Keep the retrieval latitude in `read_soi_gld()`](https://github.com/GeoPressure/GeoLocatoR/commit/315d186). The default column selection (`filter_col = TRUE`) listed `LongitudeRemoved` and `LongitudeAttached` twice and omitted `LatitudeRemoved`, so every retrieval observation created by `read_soi()` had no latitude. Packages created from SOI data with earlier versions should be recreated, or their retrieval latitudes filled. Coordinates recorded as `99999` (unknown in the SOI database) are now read as missing instead of being written as observations.
+- [Read dates from the Access file in `read_soi_gld()` on macOS and Linux](https://github.com/GeoPressure/GeoLocatoR/commit/d442338). `mdb-export` wrote them as `MM/DD/YY HH:MM:SS`, which was parsed as `NA`, so every date (attachment, retrieval, RTC, first and last data, delivery) was missing and `read_soi()` created equipment and retrieval observations without a datetime. They are now exported in ISO format. Packages created from an Access file on these systems with earlier versions should be recreated.
+
+## Minor
+
+- [Select the columns given in a character `filter_col`](https://github.com/GeoPressure/GeoLocatoR/commit/315d186) in `read_soi_gld()`, which previously always failed, and accept data frames for `data_file` and `order_file` as documented.
+- [Read `AccSamplingRate`, `PrioritySensor` and `PriorityMemory` with their actual types](https://github.com/GeoPressure/GeoLocatoR/commit/315d186) (number, text and percentage) instead of logical, which turned their values into `NA`.
+- [Warn when `read_soi()` cannot read the data of a tag](https://github.com/GeoPressure/GeoLocatoR/commit/315d186), naming the tag and the error, instead of silently leaving its measurements out.
+
+**Full Changelog**: <https://github.com/GeoPressure/GeoLocatoR/compare/v1.3.0...v1.3.1>
+
 # GeoLocatoR v1.3.0
 
 ## Main

R/read_soi.R

@@ -100,6 +100,10 @@ read_soi <- function(
             }
           },
           error = function(e) {
+            cli_warn(c(
+              "!" = "Could not read the data of tag {.val {GDL_ID}} in {.file {directory}}. Its measurements are skipped.",
+              "x" = conditionMessage(e)
+            ))
             list() # Return empty list on error
           }
         )

R/read_soi_gld.R

@@ -16,9 +16,9 @@
 #'   memory. Required when `access_file` is not provided.
 #' @param order_file Path to the GDL order file, or a data frame already loaded
 #'   in memory. Required when `access_file` is not provided.
-#' @param filter_col Logical. If `TRUE` (default), returns a predefined subset
-#'   of columns useful for package creation; if `FALSE`, returns all joined
-#'   columns.
+#' @param filter_col Logical or character vector. If `TRUE` (default), returns
+#'   a predefined subset of columns useful for package creation; if `FALSE`,
+#'   returns all joined columns; if a character vector, returns these columns.
 #'
 #' @return A data frame combining GDL tag rows and order-level information.
 #'
@@ -36,8 +36,11 @@ read_soi_gld <- function(
   order_file = NA,
   filter_col = TRUE
 ) {
-  if (!is.na(access_file)) {
-    if (!is.na(data_file) || !is.na(order_file)) {
+  # A file path or a data frame counts as provided
+  provided <- function(x) is.data.frame(x) || !(length(x) == 1 && is.na(x))
+
+  if (provided(access_file)) {
+    if (provided(data_file) || provided(order_file)) {
       cli_warn(c(
         "!" = "{.arg access_file} was provided alongside {.arg data_file} or {.arg order_file}.",
         ">" = "We'll use {.arg access_file}."
@@ -47,7 +50,7 @@ read_soi_gld <- function(
     data_file <- data_order_file[[1]]
     order_file <- data_order_file[[2]]
   } else {
-    if (is.na(data_file) || is.na(order_file)) {
+    if (!provided(data_file) || !provided(order_file)) {
       cli_abort(c(
         "x" = "Need {.arg access_file} or both {.arg data_file} and {.arg order_file}."
       ))
@@ -60,6 +63,20 @@ read_soi_gld <- function(
     d <- read_soi_gld_data(data_file)
   }
 
+  # 99999 encodes an unknown coordinate in the SOI database
+  d <- mutate(
+    d,
+    across(
+      any_of(c(
+        "LongitudeAttached",
+        "LatitudeAttached",
+        "LongitudeRemoved",
+        "LatitudeRemoved"
+      )),
+      ~ dplyr::if_else(.x == 99999, NA_real_, as.numeric(.x))
+    )
+  )
+
   if (is.data.frame(order_file)) {
     o <- order_file
   } else {
@@ -105,8 +122,7 @@ read_soi_gld <- function(
           "LatitudeAttached",
           "UTC_Removed",
           "LongitudeRemoved",
-          "LongitudeRemoved",
-          "LongitudeAttached",
+          "LatitudeRemoved",
 
           # Information needed for package
           "RingNumber",
@@ -118,7 +134,7 @@ read_soi_gld <- function(
       )
     }
   } else {
-    gdl <- select(gdl, "filter_col")
+    gdl <- select(gdl, all_of(filter_col))
   }
 
   return(gdl)
@@ -178,7 +194,7 @@ read_soi_gld_orders <- function(order_file) {
       BreastHarnessDiameterHead = readr::col_double(),
       BreastHarnessDiameterTail = readr::col_double(),
       HarnessDescription = readr::col_character(),
-      AccSamplingRate = readr::col_logical(),
+      AccSamplingRate = readr::col_double(),
       AccXaxisEnabled = readr::col_logical(),
       AccYaxisEnabled = readr::col_logical(),
       AccZaxisEnabled = readr::col_logical(),
@@ -195,7 +211,7 @@ read_soi_gld_orders <- function(order_file) {
       TRSchedule = readr::col_character(),
       LoggingSchedule = readr::col_character(),
       ActiveAfterWakeUp = readr::col_double(),
-      PrioritySensor = readr::col_logical(),
+      PrioritySensor = readr::col_character(),
       PriorityMemory = readr::col_double()
     )
   ) |>
@@ -283,8 +299,8 @@ read_soi_gld_data <- function(data_file) {
       Frequency = readr::col_double(),
       MagCalib = readr::col_character(),
       SleepCurrent = readr::col_double(),
-      PrioritySensor = readr::col_logical(),
-      PriorityMemory = readr::col_logical(),
+      PrioritySensor = readr::col_character(),
+      PriorityMemory = readr::col_double(),
       LongitudeRemoved = readr::col_double()
     )
   )
@@ -310,9 +326,18 @@ read_soi_gld_access <- function(
     ))
   }
 
+  # Exporting needs an Access file and mdb-export or the Access ODBC driver,
+  # which are not available on CI
+  # nocov start
   if (.Platform$OS.type == "unix") {
+    # mdb-export writes dates as MM/DD/YY by default, which readr cannot parse
+    # and turns into NA, so request ISO dates explicitly
+    date_args <- "-D '%Y-%m-%d' -T '%Y-%m-%d %H:%M:%S'"
+
     # Export data
-    system(glue::glue("mdb-export '{access_file}' GDL_Data > {data_file}"))
+    system(glue::glue(
+      "mdb-export {date_args} '{access_file}' GDL_Data > {data_file}"
+    ))
 
     if (!file.exists(data_file)) {
       cli_abort(c(
@@ -322,7 +347,9 @@ read_soi_gld_access <- function(
     }
 
     # Export orders
-    system(glue::glue("mdb-export '{access_file}' GDL_Orders > {order_file}"))
+    system(glue::glue(
+      "mdb-export {date_args} '{access_file}' GDL_Orders > {order_file}"
+    ))
     if (!file.exists(order_file)) {
       cli_abort(c(
         "x" = "The file {.file {order_file}} does not exist.",
@@ -347,6 +374,7 @@ read_soi_gld_access <- function(
     readr::write_csv(DBI::dbReadTable(con, "GDL_Orders"), order_file)
     readr::write_csv(DBI::dbReadTable(con, "GDL_Data"), data_file)
   }
+  # nocov end
 
   invisible(c(data_file, order_file))
 }

jarl.toml

@@ -0,0 +1,3 @@
+[lint.undesirable_operator]
+# Allow `<<-`, used deliberately to update state from closures; keep `:::` and `->>` banned
+operators = ["->>", ":::"]

tests/testthat/test-read_soi_gld.R

@@ -0,0 +1,66 @@
+test_that("read_soi_gld() keeps retrieval coordinates and handles column selection", {
+  d <- tibble(
+    OrderName = c("O1", "O1"),
+    GDL_ID = c("A1", "A2"),
+    GDL_Type = "GDL3pam",
+    Species = "Upupa epops",
+    UTC_Attached = as.POSIXct("2020-05-01", tz = "UTC"),
+    SiteAttached = "Site",
+    LongitudeAttached = 7.5,
+    LatitudeAttached = 46.2,
+    UTC_Removed = as.POSIXct("2021-05-01", tz = "UTC"),
+    LongitudeRemoved = c(8.31, 99999),
+    LatitudeRemoved = c(47.47, 99999),
+    RingNumber = c("R1", "R2"),
+    FirmwareVersion = "2.4",
+    HardwareVersion = "2.4",
+    TotalWeight = 1.5,
+    Remarks = NA_character_
+  )
+  o <- tibble(
+    OrderName = "O1",
+    NumberOrdered = 2L,
+    NumberDelivered = 2L,
+    GDL_Type = "GDL3pam",
+    Species = "Upupa epops",
+    Client = "SOI",
+    ResponsibleP3 = "P3",
+    ClientCategory = "own",
+    RemarksProduction = NA_character_,
+    RemarksOrder = NA_character_
+  )
+
+  # Default selection keeps the retrieval latitude, and 99999 is read as unknown
+  gdl <- read_soi_gld(data_file = d, order_file = o)
+  expect_true(all(c("LongitudeRemoved", "LatitudeRemoved") %in% names(gdl)))
+  expect_equal(gdl$LatitudeRemoved, c(47.47, NA))
+  expect_equal(gdl$LongitudeRemoved, c(8.31, NA))
+
+  # A character vector selects these columns
+  gdl <- read_soi_gld(data_file = d, order_file = o, filter_col = c("GDL_ID", "Client"))
+  expect_named(gdl, c("GDL_ID", "Client"))
+
+  expect_error(read_soi_gld(data_file = d), "Need")
+  expect_warning(
+    expect_error(
+      read_soi_gld(access_file = "missing.accdb", data_file = d),
+      "does not exist"
+    ),
+    "access_file"
+  )
+
+  # CSV exports are read with their declared column types; partial exports warn about the
+  # columns they lack
+  data_file <- tempfile(fileext = ".csv")
+  order_file <- tempfile(fileext = ".csv")
+  on.exit(unlink(c(data_file, order_file)), add = TRUE)
+  write.csv(mutate(d, PrioritySensor = "LIGHT", PriorityMemory = 20), data_file, row.names = FALSE)
+  write.csv(mutate(o, AccSamplingRate = 25), order_file, row.names = FALSE)
+  gdl <- suppressWarnings(
+    read_soi_gld(data_file = data_file, order_file = order_file, filter_col = FALSE)
+  )
+  expect_equal(gdl$LatitudeRemoved, c(47.47, NA))
+  expect_identical(gdl$PrioritySensor, c("LIGHT", "LIGHT"))
+  expect_identical(gdl$PriorityMemory, c(20, 20))
+  expect_identical(suppressWarnings(read_soi_gld_orders(order_file))$AccSamplingRate, 25)
+})