ruODK v0.9.1: patch geotrace/geoshape coords

* Closes #88
* Include test data snapshot with "bad" coordinates
* Test that bad coords are fixed, good coords kept
* Update news, citation, codemeta
* Add vignette "Spatial"

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: ruODK
 Title: An R Client for the ODK Central API
-Version: 0.9.0.9000
+Version: 0.9.1
 Authors@R: 
  c(person(given = c("Florian", "W."),
  family = "Mayer",

NAMESPACE

@@ -6,6 +6,7 @@ export(attachment_get)
 export(attachment_link)
 export(attachment_list)
 export(audit_get)
+export(drop_null_coords)
 export(enexpr)
 export(enquo)
 export(ensym)

NEWS.md

@@ -1,5 +1,16 @@
 # `ruODK` (development version)
 * Development continues in the default branch `main`.
+
+# `ruODK` 0.9.1
+## Major fixes
+ODK Central versions 0.7 to 0.9 export geotraces and geoshapes via OData with
+a trailing empty coordinate. `ruODK` removes any trailing empty coordinates from
+both GeoJSON and WKT formats. (#88, HT Timon Weitkamp for the bug report)
+
+## Documentation
+A new vignette "Spatial" demonstrates how to parse spatial data into native 
+formats, such as `sf`, and gives pointers on what to do next with them.
+
 
 # `ruODK` 0.9.0
 This is the release on passing 

R/data.R

@@ -391,6 +391,23 @@
 #' @encoding UTF-8
 "geo_gj"
 
+#' The parsed submissions of a form containing geofields in GeoJSON
+#' with trailing empty coordinates present.
+#'
+#' \lifecycle{stable}
+#'
+#' This issue was fixed in #88.
+#' ODK Central versions 0.7 - 0.9 export geotraces and geoshapes with trailing
+#' empty coordinates. ruODK has a patch to drop trailing empty coordinates.
+#' This dataset is used to test the patch in ruODK.
+#'
+#' @source \code{\link{odata_submission_get}(wkt=FALSE, parse=TRUE)}
+#' run on the test form
+#' `system.file("extdata", "Locations.xml", package = "ruODK")`.
+#' @family included
+#' @encoding UTF-8
+"geo_gj88"
+
 #' The unparsed submissions of a form containing geofields in WKT.
 #'
 #' \lifecycle{stable}
@@ -413,6 +430,23 @@
 #' @encoding UTF-8
 "geo_wkt"
 
+#' The parsed submissions of a form containing geofields in WKT
+#' with trailing empty coordinates present.
+#'
+#' \lifecycle{stable}
+#'
+#' This issue was fixed in #88.
+#' ODK Central versions 0.7 - 0.9 export geotraces and geoshapes with trailing
+#' empty coordinates. ruODK has a patch to drop trailing empty coordinates.
+#' This dataset is used to test the patch in ruODK.
+#'
+#' @source \code{\link{odata_submission_get}(wkt=TRUE, parse=TRUE)}
+#' run on the test form
+#' `system.file("extdata", "Locations.xml", package = "ruODK")`.
+#' @family included
+#' @encoding UTF-8
+"geo_wkt88"
+
 #' The unparsed XML form_schema of a form from ODK Central v0.6 as nested list.
 #'
 #' \lifecycle{stable}

R/drop_null_coords.R

@@ -0,0 +1,60 @@
+#' Drop any NULL coordinates from a GeoJSON geometry.
+#'
+#' This helper patches a bug/feature in ODK Central (versions 0.7-0.9), where
+#' geotrace / geoshape GeoJSON contains a last coordinate pair with NULL
+#' lat/lon (no alt/acc), and WKT ends in `, undefined NaN`.
+#'
+#' While \code{\link{split_geotrace}} and \code{\link{split_geoshape}} modify
+#' the WKT inline, it is more maintainable to separate the GeoJSON cleaner
+#' into this function.
+#'
+#' This helper drops the last element of a GeoJSON coordinate list if it is
+#' `list(NULL, NULL)`.
+#'
+#' @param x A GeoJSON geometry parsed as nested list.
+#' E.g. `geo_gj$path_location_path_gps`.
+#' @return The nested list minus the last element (if NULL).
+#' @family utilities
+#' @export
+#' @examples
+#' # A snapshot of geo data with trailing empty coordinates.
+#' data("geo_gj88")
+#'
+#' len_coords <- length(geo_gj88$path_location_path_gps[[1]]$coordinates)
+#'
+#' length(geo_gj88$path_location_path_gps[[1]]$coordinates[[len_coords]]) %>%
+#' testthat::expect_equal(2)
+#'
+#' geo_gj88$path_location_path_gps[[1]]$coordinates[[len_coords]][[1]] %>%
+#' testthat::expect_null()
+#'
+#' geo_gj88$path_location_path_gps[[1]]$coordinates[[len_coords]][[2]] %>%
+#' testthat::expect_null()
+#'
+#' # The last coordinate pair is a list(NULL, NULL).
+#' # Invalid coordinates like these are a choking hazard for geospatial
+#' # packages. We should remove them before we can convert ODK data into native
+#' # spatial formats, such as sf.
+#' str(geo_gj88$path_location_path_gps[[1]]$coordinates[[len_coords]])
+#'
+#' geo_gj_repaired <- geo_gj88 %>%
+#' dplyr::mutate(
+#' path_location_path_gps = path_location_path_gps %>%
+#' purrr::map(drop_null_coords)
+#' )
+#'
+#' len_coords_repaired <- length(
+#' geo_gj_repaired$path_location_path_gps[[1]]$coordinates
+#' )
+#' testthat::expect_equal(len_coords_repaired + 1, len_coords)
+drop_null_coords <- function(x) {
+ # Extract and simplify last coords. list(NULL, NULL) becomes list().
+ xx <- purrr::compact(x$coordinates[[length(x$coordinates)]])
+ # Remove empty coords by setting the entire list(NULL, NULL) to NULL.
+ if (is.list(xx) && length(xx) == 0) {
+ x$coordinates[[length(x$coordinates)]] <- NULL
+ }
+ x
+}
+
+# usethis::use_test("drop_null_coords") # nolint

R/split_geoshape.R

@@ -69,17 +69,16 @@
 #' )
 #' }
 split_geoshape <- function(
- data,
- colname,
- wkt = FALSE,
- odkc_version = odkc_version
-) {
+ data,
+ colname,
+ wkt = FALSE,
+ odkc_version = odkc_version) {
  if (nrow(data) == 0) {
  # Option 1: Early exit - nothing to do
  return(data)
  } else if (odkc_version < 0.8) {
  # Option 2: ODK linestring
- # ODK Central <=0.7 ignores the WKT argument for geotrace and geoshape
+ # ODK Central <=0.7 ignores the WKT argument for geotrace and geoshape.
  # nolint start
  # ruODK::odata_submission_get(wkt = TRUE, parse = TRUE)
  # ruODK::odata_submission_get(wkt = FALSE, parse = FALSE) %>%
@@ -116,8 +115,13 @@ split_geoshape <- function(
  dplyr::rename_at(
  dplyr::vars(dplyr::starts_with("XXX")),
  list(~ stringr::str_replace(., "XXX", colname))
+ ) %>%
+ # Drop last empty coordinate from colname, a list(NULL, NULL).
+ # Affects ODK Central Version 0.7-0.9.
+ dplyr::mutate_at(
+ dplyr::vars(colname),
+ list(~ purrr::map(., drop_null_coords))
  )
- # TODO #88 drop last empty coord from colname
  } else {
  # WKT
  data %>%
@@ -132,6 +136,8 @@ split_geoshape <- function(
  remove = FALSE,
  convert = TRUE
  ) %>%
+ # Drop last empty coordinate from colname, a trailing ",undefined NaN".
+ # Affects ODK Central Version 0.7-0.9.
  dplyr::mutate_at(
  dplyr::vars(colname),
  list(~ stringr::str_replace_all(., ",undefined NaN", ""))

R/split_geotrace.R

@@ -130,8 +130,13 @@ split_geotrace <- function(data,
  dplyr::rename_at(
  dplyr::vars(dplyr::starts_with("XXX")),
  list(~ stringr::str_replace(., "XXX", colname))
+ ) %>%
+ # Drop last empty coordinate from colname, a list(NULL, NULL).
+ # Affects ODK Central Version 0.7-0.9.
+ dplyr::mutate_at(
+ dplyr::vars(colname),
+ list(~ purrr::map(., drop_null_coords))
  )
- # TODO #88 drop last empty coord from colname
  } else {
  # Option 4: ODKC v0.8 WKT
  data %>%

codemeta.json

@@ -14,11 +14,10 @@
  ],
  "issueTracker": "https://github.com/ropensci/ruODK/issues",
  "license": "https://spdx.org/licenses/GPL-3.0",
- "version": "0.9.0",
+ "version": "0.9.1",
  "programmingLanguage": {
  "@type": "ComputerLanguage",
  "name": "R",
- "version": "4.0.0",
  "url": "https://r-project.org"
  },
  "runtimePlatform": "R version 4.0.0 (2020-04-24)",
@@ -136,6 +135,19 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=listviewer"
  },
+ {
+ "@type": "SoftwareApplication",
+ "identifier": "mapview",
+ "name": "mapview",
+ "version": ">= 2.7.8",
+ "provider": {
+ "@id": "https://cran.r-project.org",
+ "@type": "Organization",
+ "name": "Comprehensive R Archive Network (CRAN)",
+ "url": "https://cran.r-project.org"
+ },
+ "sameAs": "https://CRAN.R-project.org/package=mapview"
+ },
  {
  "@type": "SoftwareApplication",
  "identifier": "rmarkdown",
@@ -162,6 +174,19 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=roxygen2"
  },
+ {
+ "@type": "SoftwareApplication",
+ "identifier": "sf",
+ "name": "sf",
+ "version": ">= 0.9-5",
+ "provider": {
+ "@id": "https://cran.r-project.org",
+ "@type": "Organization",
+ "name": "Comprehensive R Archive Network (CRAN)",
+ "url": "https://cran.r-project.org"
+ },
+ "sameAs": "https://CRAN.R-project.org/package=sf"
+ },
  {
  "@type": "SoftwareApplication",
  "identifier": "testthat",
@@ -472,28 +497,17 @@
  ],
  "name": "ruODK: Client for the ODK Central API",
  "url": "https://github.com/ropensci/ruODK",
- "description": "R package version 0.9.0"
+ "description": "R package version 0.9.1"
  }
  ],
  "releaseNotes": "https://github.com/ropensci/ruODK/blob/master/NEWS.md",
  "readme": "https://github.com/ropensci/ruODK/blob/main/README.md",
- "fileSize": "1010.359KB",
- "contIntegration": [
- "https://travis-ci.org/ropensci/ruODK",
- "https://ci.appveyor.com/project/florianm/ruodk/branch/master",
- "https://codecov.io/github/ropensci/ruODK?branch=master",
- "https://travis-ci.org/ropensci/ruODK",
- "https://codecov.io/github/ropensci/ruODK?branch=master",
- "https://ci.appveyor.com/project/florianm/ruodk/branch/master",
- "https://codecov.io/gh/validmeasures/odkr",
- "https://travis-ci.org/unhcr/koboloadeR",
- "https://ci.appveyor.com/project/unhcr/koboloadeR",
- "https://codecov.io/gh/unhcr/koboloadeR",
- "https://travis-ci.org/ropensci/ruODK",
- "https://ci.appveyor.com/project/florianm/ruodk/branch/master",
- "https://codecov.io/github/ropensci/ruODK?branch=master",
- "https://travis-ci.org/edwindj/cbsodataR",
- "https://ci.appveyor.com/project/edwindj/cbsodatar"
- ],
- "developmentStatus": "https://www.repostatus.org/#active"
+ "fileSize": "3126.119KB",
+ "contIntegration": ["https://travis-ci.org/ropensci/ruODK", "https://ci.appveyor.com/project/florianm/ruodk/branch/main", "https://codecov.io/gh/ropensci/ruODK", "https://travis-ci.org/ropensci/ruODK", "https://codecov.io/gh/ropensci/ruODK", "https://ci.appveyor.com/project/florianm/ruodk/branch/main", "https://codecov.io/gh/validmeasures/odkr", "https://travis-ci.org/unhcr/koboloadeR", "https://ci.appveyor.com/project/unhcr/koboloadeR", "https://codecov.io/gh/unhcr/koboloadeR", "https://travis-ci.org/ropensci/ruODK", "https://ci.appveyor.com/project/florianm/ruodk/branch/main", "https://codecov.io/gh/ropensci/ruODK", "https://travis-ci.org/edwindj/cbsodataR", "https://ci.appveyor.com/project/edwindj/cbsodatar"],
+ "developmentStatus": "https://www.repostatus.org/#active",
+ "review": {
+ "@type": "Review",
+ "url": "https://github.com/ropensci/software-review/issues/335",
+ "provider": "https://ropensci.org"
+ }
 }

data-raw/make_release.R

@@ -19,8 +19,8 @@ source(here::here("data-raw/make_data.R"))
 devtools::test()
 #
 # Docs
-lintr:::addin_lint_package()
 styler::style_pkg()
+lintr:::addin_lint_package()
 devtools::document(roclets = c("rd", "collate", "namespace"))
 spelling::spell_check_package()
 spelling::spell_check_files("README.Rmd", lang = "en_AU") # TODO update wordlist

inst/CITATION

@@ -4,12 +4,12 @@ citEntry(
  entry = "Misc",
  title = "ruODK: Client for the ODK Central API",
  author = "Florian W. Mayer",
- note = "R package version 0.9.0",
+ note = "R package version 0.9.1",
  year = 2020,
  url = "https://github.com/ropensci/ruODK",
  textVersion = paste(
  "Mayer, Florian Wendelin. (2020, July 21). ",
- "ruODK: An R Client for the ODK Central API (Version 0.9.0). ",
+ "ruODK: An R Client for the ODK Central API (Version 0.9.1). ",
  "Zenodo. http://doi.org/10.5281/zenodo.3953159"
  )
 )