Merge pull request #15 from inbo/first_functions

Add first functions to support reading Camtrap DP

.Rbuildignore

@@ -3,3 +3,6 @@
 ^LICENSE\.md$
 ^\.github$
 ^README\.Rmd$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -48,3 +48,6 @@ po/*~
 # RStudio Connect folder
 rsconnect/
 .Rproj.user
+
+# Mac OS
+.DS_Store

DESCRIPTION

@@ -2,18 +2,25 @@ Package: camtrapdp
 Title: Read and Convert Camera Trap Data Packages (Camtrap DP)
 Version: 0.0.0.9000
 Authors@R: c(
+    person("Peter", "Desmet", email = "[email protected]",
+           role = c("aut", "cre"), comment =  c(ORCID = "0000-0002-8442-8025")),
     person("Damiano", "Oldoni", email = "[email protected]",
-           role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3445-7562")),
+           role = "aut", comment = c(ORCID = "0000-0003-3445-7562")),
     person("Research Institute for Nature and Forest (INBO)",
            role = "cph", comment = "https://www.vlaanderen.be/inbo/en-gb/"),
     person("LifeWatch Belgium",
            role = "fnd", comment = "https://lifewatch.be")
   )
 Description: What the package does (one paragraph).
 License: MIT + file LICENSE
+URL: https://github.com/inbo/camtrapdp, https://inbo.github.io/camtrapdp/
+BugReports: https://github.com/inbo/camtrapdp/issues
+Imports:
+    cli,
+    frictionless
+Suggests: 
+    testthat (>= 3.0.0)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.0
-Suggests: 
-    testthat (>= 3.0.0)
 Config/testthat/edition: 3

NAMESPACE

@@ -1,2 +1,4 @@
 # Generated by roxygen2: do not edit by hand
 
+export(read_camtrap_dp)
+export(version)

R/convert.R

@@ -0,0 +1,28 @@
+#' Convert a Camera Trap Data Package
+#'
+#' Converts a Camera Trap Data Package object that uses an older version of
+#' the Camtrap DP standard to a newer version.
+#'
+#' @inheritParams version
+#' @param convert_to Version to convert to.
+#' @return Converted Camera Trap Data Package object.
+#' @noRd
+convert <- function(x, convert_to = "1.0") {
+  # Convert until the version number matches the expected version
+  while(version(x) != convert_to) {
+    x <- switch(
+      version(x),
+      "0.1.6" = convert_0.1.6_to_1.0(x),
+      "1.0" = x
+    )
+  }
+  x
+}
+
+#' Convert a Camtrap DP 0.1.6 to 1.0
+#' @noRd
+convert_0.1.6_to_1.0 <- function(x) {
+  # TODO: conversion steps for 0.1.6
+  attr(x, "version") <- "1.0"
+  x
+}

R/read_camtrap_dp.R

@@ -0,0 +1,41 @@
+#' Read a Camera Trap Data Package
+#'
+#' Reads files from a [Camera Trap Data Package (Camtrap DP)](
+#' https://camtrap-dp.tdwg.org) into memory.
+#'
+#' @param file Path or URL to a `datapackage.json` file.
+#' @return Camera Trap Data Package object.
+#' @export
+read_camtrap_dp <- function(file) {
+  # Read datapackage.json
+  package <- frictionless::read_package(file)
+
+  # Check version
+  version <- version(package)
+  supported_versions <- c("1.0")
+  if (!version %in% supported_versions) {
+    cli::cli_abort(
+      c(
+        "{.val {version}} is not a supported Camtrap DP version.",
+        "i" = "Supported version{?s}: {.val {supported_versions}}."
+      ),
+      class = "camtrapdp_error_unsupported_version"
+    )
+  }
+
+  # Create camtrapdp object
+  x <- package
+  class(x) <- c("camtrapdp", class(x))
+  attr(x, "version") <- version
+
+  # Read and attach csv data
+  x$data$deployments <-
+    frictionless::read_resource(package, "deployments")
+  x$data$media <-
+    frictionless::read_resource(package, "media")
+  x$data$observations <-
+    frictionless::read_resource(package, "observations")
+
+  # Convert
+  convert(x, convert_to = "1.0")
+}

R/version.R

@@ -0,0 +1,44 @@
+#' Get Camtrap DP version
+#'
+#' Extracts the version number used by a Camera Trap Data Package object.
+#' This version number indicates what version of the [Camtrap DP standard](
+#' https://camtrap-dp.tdwg.org) was used.
+#'
+#' The version number is derived as follows:
+#' 1. The `version` attribute, if defined.
+#' 2. A version number contained in `x$profile`, which is expected to
+#' contain the URL to the used Camtrap DP standard.
+#' 3. `x$profile` in its entirety (can be `NULL`).
+#'
+#' @param x Camera Trap Data Package object, as returned by
+#'   `read_camtrap_dp()`.
+#'   Also works on a Frictionless Data Package, as returned by
+#'   `frictionless::read_package()`.
+#' @return Camtrap DP version number (e.g. `1.0`).
+#' @export
+version <- function(x) {
+  # Get version from attribute
+  attr_version <- attr(x, "version")
+  if (!is.null(attr_version)) {
+    return(attr_version)
+  }
+
+  # Get version from profile
+  profile <- x$profile
+  if (is.null(profile)) {
+    return(NA)
+  }
+
+  # Find pattern "camtrap-dp/<version>/" in e.g.
+  # https://raw.githubusercontent.com/tdwg/camtrap-dp/1.0/camtrap-dp-profile.json
+  pattern <- "camtrap-dp\\/([0-9A-Za-z]|\\.|-)+\\/"
+  match <- grep(pattern, profile)
+  if (length(match) > 0) {
+    extracted_version <- regmatches(profile, regexpr(pattern, profile))
+    extracted_version <- sub("camtrap-dp/", "", extracted_version, fixed = TRUE)
+    extracted_version <- sub("/", "", extracted_version, fixed = TRUE)
+    extracted_version
+  } else {
+    profile
+  }
+}

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://inbo.github.io/camtrapdp/
+template:
+  bootstrap: 5
+

tests/testthat/test-read_camtrap_dp.R

@@ -1,3 +1,40 @@
-test_that("multiplication works", {
-  expect_equal(2 * 2, 4)
+test_that("read_camtrap_dp() reads a Camtrap DP", {
+  skip_if_offline()
+  file <-
+    "https://raw.githubusercontent.com/tdwg/camtrap-dp/1.0/example/datapackage.json"
+  expect_no_error(read_camtrap_dp(file))
+
+  # TODO: add more tests on returned object
+})
+
+test_that("read_camtrap_dp() returns error on unsupported Camtrap DP version", {
+  skip_if_offline()
+
+  # Unsupported version
+  camtrap_dp_1.0_rc.1 <-
+    "https://raw.githubusercontent.com/tdwg/camtrap-dp/1.0-rc.1/example/datapackage.json"
+  expect_error(
+    read_camtrap_dp(camtrap_dp_1.0_rc.1),
+    class = "camtrapdp_error_unsupported_version"
+  )
+  expect_error(
+    read_camtrap_dp(camtrap_dp_1.0_rc.1),
+    regexp = "\"1.0-rc.1\" is not a supported Camtrap DP version.",
+    fixed = TRUE
+  )
+
+  # Not a Camtrap DP
+  o_assen <- "https://zenodo.org/records/10053903/files/datapackage.json"
+  expect_error(
+    read_camtrap_dp(o_assen),
+    class = "camtrapdp_error_unsupported_version"
+  )
+})
+
+test_that("read_camtrap_dp() does not convert 1.0", {
+  skip_if_offline()
+  camtrap_dp_1.0 <-
+    "https://raw.githubusercontent.com/tdwg/camtrap-dp/1.0/example/datapackage.json"
+  x <- read_camtrap_dp(camtrap_dp_1.0)
+  expect_identical(version(x), "1.0")
 })

tests/testthat/test-version.R

@@ -0,0 +1,35 @@
+test_that("version() extracts version from attribute", {
+  x <- list()
+  attr(x, "version") <- "1.0"
+  expect_identical(version(x), "1.0")
+})
+
+test_that("version() extracts version from x$profile on match", {
+  x <- list()
+  x$profile <- "https://raw.githubusercontent.com/tdwg/camtrap-dp/1.0/camtrap-dp-profile.json"
+  expect_identical(version(x), "1.0")
+  x$profile <- "https://rs.gbif.org/sandbox/data-packages/camtrap-dp/1.0/profile/camtrap-dp-profile.json"
+  expect_identical(version(x), "1.0")
+  x$profile <- "foo/camtrap-dp/2/foo"
+  expect_identical(version(x), "2")
+  x$profile <- "foo/camtrap-dp/2.30/foo"
+  expect_identical(version(x), "2.30")
+  x$profile <- "foo/camtrap-dp/2.30.5/foo"
+  expect_identical(version(x), "2.30.5")
+  x$profile <- "foo/camtrap-dp/1.0-rc.1/foo"
+  expect_identical(version(x), "1.0-rc.1")
+})
+
+test_that("version() returns x$profile when no match is found", {
+  x <- list()
+  x$profile <- NULL
+  expect_identical(version(x), NA)
+  x$profile <- NA
+  expect_identical(version(x), NA)
+  x$profile <- 1
+  expect_identical(version(x), 1)
+  x$profile <- "tabular-data-package"
+  expect_identical(version(x), "tabular-data-package")
+  x$profile <- "foo/2.30/foo" # Must contain camtrap-dp/<version>
+  expect_identical(version(x), "foo/2.30/foo")
+})