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"
   )
 )