Merge pull request #296 from inbo/improve-version-detection

Improve version detection

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: camtraptor
 Title: Read, Explore and Visualize Camera Trap Data Packages
-Version: 0.24.0
+Version: 0.25.0
 Authors@R: c(
     person("Damiano", "Oldoni", email = "[email protected]",
            role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3445-7562")),

NEWS.md

@@ -1,3 +1,21 @@
+# camtraptor 0.25.0
+
+- `read_camtrap_dp()` detects Camtrap DP version from `package$profile` using 
+regex (#295).
+This supports reading Camtrap DPs created by the GBIF IPT.
+
+# camtraptor 0.24.0
+
+- Replicate old Camtrap DP 0.1.6 behaviour and populate `angle` and `radius` for 
+event-based observations.
+Values are taken from the first media-based observation (fields 
+`individualPositionRadius` and `individualPositionAngle`) for each 
+`eventID/individualID` combination (#291).
+
+# camtraptor 0.23.0
+
+- Fix bug in `read_camtrap_dp()` when reading a Camtrap DP 1.0 (#292).
+
 # camtraptor 0.22.0
 
 - Fix bug in `write_eml()` for Camtrap DP 1.0 datasets (#290).
@@ -6,10 +24,10 @@
 
 # camtraptor 0.21.0
 
-- `read_camtrap_dp()` supports Camtrap DP 1.0 (upcoming Agouti export format) 
-  in favour of Camtrap DP 1.0-rc.1 (#284).
-  To avoid breaking changes to users, it will down-convert Camtrap DP 1.0 to
-  0.1.6 which is currently used as internal data model for camtraptor.
+- `read_camtrap_dp()` supports Camtrap DP 1.0 (upcoming Agouti export format) in 
+favour of Camtrap DP 1.0-rc.1 (#284).
+To avoid breaking changes to users, it will down-convert Camtrap DP 1.0 to 0.1.6
+which is currently used as internal data model for camtraptor.
 - `get_custom_effort()` now calculates per calendar month/week (#219).
 - `write_dwc()` has an updated mapping for dwc_audubon.csv (#274).
 - `get_record_table()` returns the number of observed individuals (#279).

R/read_camtrap_dp.R

@@ -49,7 +49,7 @@
 read_camtrap_dp <- function(file = NULL,
                             media = TRUE,
                             path = lifecycle::deprecated()) {
-  # check path (deprecated)
+  # Check path (deprecated)
   warning_detail <- paste(
     "Use argument `file` containing the path or URL to the `datapackage.json`",
     "file. The use of parameter `path` with path to the local directory is ",
@@ -62,39 +62,26 @@ read_camtrap_dp <- function(file = NULL,
       details = warning_detail
     )
   }
-  # define the right file value
+  # Define the right file value
   if (lifecycle::is_present(path)) {
     file <- file.path(path, "datapackage.json")
   }
-  # file value is a valid path
+  # File value is a valid path
   if (dir.exists(file)) {
     file <- file.path(file, "datapackage.json")
   }
-  # check media arg
+  # Check media arg
   assertthat::assert_that(
     media %in% c(TRUE, FALSE),
     msg = "`media` must be a logical: TRUE or FALSE"
   )
 
-  # read package (metadata)
+  # Read package (metadata)
   package <- frictionless::read_package(file)
 
-  # supported versions
+  # Check Camtrap DP version is supported
+  version <- get_version(profile = package$profile)
   supported_versions <- c("0.1.6", "1.0")
-
-  # get package version
-  profile <- package$profile
-  if (profile == "https://raw.githubusercontent.com/tdwg/camtrap-dp/1.0/camtrap-dp-profile.json") {
-    version <- "1.0"
-  } else {
-    if (profile == "https://raw.githubusercontent.com/tdwg/camtrap-dp/0.1.6/camtrap-dp-profile.json") {
-      version <- "0.1.6"
-    } else {
-      version <- profile
-    }
-  }
-
-  # check version is supported
   assertthat::assert_that(
     version %in% supported_versions,
     msg = glue::glue(
@@ -103,9 +90,10 @@ read_camtrap_dp <- function(file = NULL,
     )
   )
 
-  # get resource names
+  # Get resource names
   resource_names <- frictionless::resources(package)
-  #check needed resources are present
+
+  # Check needed resources are present
   resources_to_read <- c("deployments", "media", "observations")
   assertthat::assert_that(
     all(resources_to_read %in% resource_names),
@@ -116,18 +104,18 @@ read_camtrap_dp <- function(file = NULL,
     )
   )
 
-  # read deployments
+  # Read deployments
   deployments <- frictionless::read_resource(package, "deployments")
   issues_deployments <- check_reading_issues(deployments, "deployments")
-  # read observations (needed to create sequenceID in media)
+  # Read observations (needed to create sequenceID in media)
   observations <- frictionless::read_resource(package, "observations")
   issues_observations <- check_reading_issues(observations, "observations")
 
   if (version == "0.1.6"){
     observations <- add_speed_radius_angle(observations)
   }
 
-  # create first version datapackage with resources in data slot
+  # Create first version datapackage with resources in data slot
   data <- list(
     "deployments" = deployments,
     "media" = NULL,
@@ -136,7 +124,7 @@ read_camtrap_dp <- function(file = NULL,
 
   package$data <- data
 
-  # read media if needed
+  # Read media if needed
   if (media) {
     media_df <- frictionless::read_resource(package, "media")
     issues_media <- check_reading_issues(media_df, "media")
@@ -148,12 +136,12 @@ read_camtrap_dp <- function(file = NULL,
 
   package <- add_taxonomic_info(package)
 
-  # convert to 0.1.6
+  # Convert to 0.1.6
   if (version == "1.0") {
     package <- convert_to_0.1.6(package, version, media = media)
   }
 
-  # order columns
+  # Order columns
   package$data$deployments <- order_cols_deployments(package$data$deployments)
   package$data$observations <- order_cols_observations(
     package$data$observations

R/zzz.R

@@ -70,6 +70,33 @@ check_value <- function(arg, options = NULL, arg_name, null_allowed = TRUE) {
   }
 }
 
+#' Get version from data package profile
+#'
+#' This helper functions returns the version of a Camera Trap Data Package by
+#' applying a regex to its `profile`.
+#' 
+#' The regex rule extracts the version by detecting a sequence of digits and dots.
+#' If no dots are detected or `"camtrap-dp-profile.json"` is not part of
+#' `profile`, the entire `profile` is returned.
+#' 
+#' @param profile Character containing the profile of the data package.
+#' @return Character containing the data package version.
+#' @noRd
+get_version <- function(profile) {
+  pattern_regex <- "\\d+(\\.\\d+){1,2}" # a sequence of digits and dots (max 2)
+  extracted_version <- stringr::str_extract(
+    string = profile, 
+    pattern = pattern_regex
+  )
+  if (stringr::str_detect(string = profile, 
+                          pattern = stringr::fixed("camtrap-dp-profile.json")) & 
+      !is.na(extracted_version)) {
+    extracted_version
+  } else {
+    profile
+  }
+}
+
 #' Check reading issues
 #' 
 #' This helper function throws a warning if issues while reading datapackage
@@ -78,8 +105,9 @@ check_value <- function(arg, options = NULL, arg_name, null_allowed = TRUE) {
 #' 
 #' @param df Data.frame.
 #' @param df_name Character with name of the data.frame passed to `df`.
-#' @noRd
 #' @return Data.frame containing the issues as returned by `readr::problems()`.
+#' @noRd
+#' 
 check_reading_issues <- function(df, df_name) {
   # get problems
   issues_df <- readr::problems(df)

tests/testthat/test-read_camtrap_dp.R

@@ -31,7 +31,7 @@ test_that("file can be an URL", {
 test_that("only DP versions 1.0 and dp 0.1.6 are supported", {
   expect_error(
     suppressMessages(read_camtrap_dp("https://raw.githubusercontent.com/tdwg/camtrap-dp/bb046c85a55bef2ced709357c0047f0136df8326/example/datapackage.json")),
-    "Version `https://raw.githubusercontent.com/tdwg/camtrap-dp/0.5/camtrap-dp-profile.json` is not supported. Supported versions: 0.1.6 and 1.0",
+    "Version `0.5` is not supported. Supported versions: 0.1.6 and 1.0",
     fixed = TRUE
   )