Merge pull request #180 from whitehacker/master

Add warning for unset 'where' argument in toolGetMapping function
pik-piam · Sep 28, 2023 · 4d7fcc6 · 4d7fcc6
2 parents 826d4b1 + ff36152
commit 4d7fcc6
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Showing 7 changed files with 45 additions and 28 deletions.
diff --git a/.buildlibrary b/.buildlibrary
@@ -1,4 +1,4 @@
-ValidationKey: '7159110'
+ValidationKey: '7183116'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

diff --git a/CITATION.cff b/CITATION.cff
@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'madrat: May All Data be Reproducible and Transparent (MADRaT) *'
-version: 3.6.5
-date-released: '2023-09-14'
+version: 3.6.6
+date-released: '2023-09-26'
 abstract: Provides a framework which should improve reproducibility and transparency
   in data processing. It provides functionality such as automatic meta data creation
   and management, rudimentary quality management, data caching, work-flow management

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: madrat
 Title: May All Data be Reproducible and Transparent (MADRaT) *
-Version: 3.6.5
-Date: 2023-09-14
+Version: 3.6.6
+Date: 2023-09-26
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "[email protected]", role = c("aut", "cre")),
     person("Lavinia", "Baumstark", , "[email protected]", role = "aut"),

diff --git a/R/toolGetMapping.R b/R/toolGetMapping.R
@@ -30,8 +30,15 @@ toolGetMapping <- function(name, type = NULL, where = NULL,
                            error.missing = TRUE, # nolint
                            returnPathOnly = FALSE, activecalc = NULL) {
 
+  if (isWrapperActive("wrapperChecks")) {
+    for (w in c("downloadSource", "readSource", "calcOutput", "retrieveData")) {
+      if (isWrapperActive(w) && is.null(where)) {
+        warning("argument 'where' should be set when calling toolGetMapping from within a madrat function.")
+        break
+      }
+    }
+  }
   setWrapperInactive("wrapperChecks")
-
   fname <- .searchName(name = name, type = type, where = where, activecalc = activecalc)
 
   if (error.missing && !file.exists(as.character(fname))) stop('Mapping "', name, '" not found!')

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # May All Data be Reproducible and Transparent (MADRaT) *
 
-R package **madrat**, version **3.6.5**
+R package **madrat**, version **3.6.6**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/madrat)](https://cran.r-project.org/package=madrat) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1115490.svg)](https://doi.org/10.5281/zenodo.1115490) [![R build status](https://github.com/pik-piam/madrat/workflows/check/badge.svg)](https://github.com/pik-piam/madrat/actions) [![codecov](https://codecov.io/gh/pik-piam/madrat/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/madrat) [![r-universe](https://pik-piam.r-universe.dev/badges/madrat)](https://pik-piam.r-universe.dev/builds)
 
@@ -55,7 +55,7 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **madrat** in publications use:
 
-Dietrich J, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Leip D, Kreidenweis U, Klein D, Führlich P (2023). _madrat: May All Data be Reproducible and Transparent (MADRaT)_. doi:10.5281/zenodo.1115490 <https://doi.org/10.5281/zenodo.1115490>, R package version 3.6.5, <https://github.com/pik-piam/madrat>.
+Dietrich J, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Leip D, Kreidenweis U, Klein D, Führlich P (2023). _madrat: May All Data be Reproducible and Transparent (MADRaT)_. doi:10.5281/zenodo.1115490 <https://doi.org/10.5281/zenodo.1115490>, R package version 3.6.6, <https://github.com/pik-piam/madrat>.
 
 A BibTeX entry for LaTeX users is
 
@@ -64,7 +64,7 @@ A BibTeX entry for LaTeX users is
   title = {madrat: May All Data be Reproducible and Transparent (MADRaT)},
   author = {Jan Philipp Dietrich and Lavinia Baumstark and Stephen Wirth and Anastasis Giannousakis and Renato Rodrigues and Benjamin Leon Bodirsky and Debbora Leip and Ulrich Kreidenweis and David Klein and Pascal Führlich},
   year = {2023},
-  note = {R package version 3.6.5},
+  note = {R package version 3.6.6},
   doi = {10.5281/zenodo.1115490},
   url = {https://github.com/pik-piam/madrat},
 }

diff --git a/tests/testthat/test-calcOutput.R b/tests/testthat/test-calcOutput.R
@@ -117,11 +117,11 @@ test_that("Calculation for tau example data set works", {
   require(magclass)
   localConfig(ignorecache = FALSE, forcecache = FALSE, verbosity = 2)
   expectedResult <- new("magpie",
-                         .Data = structure(c(0.99, 0.83, 0.68, 1.47, 0.9, 0.64, 0.8, 0.97, 1.17, 0.89, 1.27, 1.25),
-                                           .Dim = c(12L, 1L, 1L),
-                                           .Dimnames = list(region = c("LAM", "OAS", "SSA", "EUR", "NEU", "MEA",
-                                                                       "REF", "CAZ", "CHA", "IND", "JPN", "USA"),
-                                                            year = NULL, data = NULL)))
+                        .Data = structure(c(0.99, 0.83, 0.68, 1.47, 0.9, 0.64, 0.8, 0.97, 1.17, 0.89, 1.27, 1.25),
+                                          .Dim = c(12L, 1L, 1L),
+                                          .Dimnames = list(region = c("LAM", "OAS", "SSA", "EUR", "NEU", "MEA",
+                                                                      "REF", "CAZ", "CHA", "IND", "JPN", "USA"),
+                                                           year = NULL, data = NULL)))
   x <- calcOutput("TauTotal", source = "historical", years = 1995, round = 2, supplementary = TRUE)
   expect_true(is.list(x))
   expect_equivalent(x$x, expectedResult)
@@ -147,11 +147,11 @@ test_that("Standard workflow works", {
   }
   fullTEST2 <- function(rev = 0, dev = "") {
     expectedOutput <- new("magpie",
-                           .Data = structure(c(540, 490, 510, 331, 160, 210, 120, 50, 40, 10, 10, 10),
-                                             .Dim = c(12L, 1L, 1L),
-                                             .Dimnames = list(fake = c("LAM", "OAS", "SSA", "EUR", "NEU", "MEA", "REF",
-                                                                       "CAZ", "CHA", "IND", "JPN", "USA"),
-                                                              year = NULL, data = NULL)))
+                          .Data = structure(c(540, 490, 510, 331, 160, 210, 120, 50, 40, 10, 10, 10),
+                                            .Dim = c(12L, 1L, 1L),
+                                            .Dimnames = list(fake = c("LAM", "OAS", "SSA", "EUR", "NEU", "MEA", "REF",
+                                                                      "CAZ", "CHA", "IND", "JPN", "USA"),
+                                                             year = NULL, data = NULL)))
 
     expect_warning(co <- capture.output(a <- calcOutput("Test2", file = "test.mz")),
                    'Missing description for data set "Test2"')
@@ -268,15 +268,17 @@ test_that("Aggregation works", {
                                                                      "JPN", "USA"),
                                                           year = NULL, data = NULL)))
   glo <- new("magpie", .Data = structure(249, .Dim = c(1L, 1L, 1L),
-              .Dimnames = list(region = "GLO", year = NULL, data = NULL)))
+                                         .Dimnames = list(region = "GLO", year = NULL, data = NULL)))
 
-  country2 <- new("magpie", .Data = structure(rep(8, 249), .Dim = c(249L, 1L, 1L), .Dimnames = list(
-    country = unname(getISOlist()), year = NULL, data = NULL)))
+  country2 <- new("magpie", .Data = structure(rep(8, 249), .Dim = c(249L, 1L, 1L),
+                                              .Dimnames = list(country = unname(getISOlist()),
+                                                               year = NULL, data = NULL)))
 
   reg2 <- new("magpie", .Data = structure(c(432, 392, 408, 272, 128, 168,
-                                            96, 40, 32, 8, 8, 8), .Dim = c(12L, 1L, 1L), .Dimnames = list(
-                                            region = c("LAM", "OAS", "SSA", "EUR", "NEU", "MEA", "REF",
-                                                       "CAZ", "CHA", "IND", "JPN", "USA"), year = NULL, data = NULL)))
+                                            96, 40, 32, 8, 8, 8), .Dim = c(12L, 1L, 1L),
+                                          .Dimnames = list(region = c("LAM", "OAS", "SSA", "EUR", "NEU", "MEA",
+                                                                      "REF", "CAZ", "CHA", "IND", "JPN", "USA"),
+                                                           year = NULL, data = NULL)))
   glo2 <- new("magpie", .Data = structure(1992, .Dim = c(1L, 1L, 1L),
                                           .Dimnames = list(global = "GLO", year = NULL, data = NULL)))
 
@@ -308,8 +310,8 @@ test_that("Aggregation works", {
     # set verbosity to a level that will produce the expected NOTE
     localConfig(verbosity = 1)
     expect_message(a <- nc(calcOutput("AggregationTest", aggregate = "glo")),
-      paste0("Ignoring column\\(s\\) X, region, global from .* as the column\\(s\\) ",
-      "already exist in another mapping\\."))
+                   paste0("Ignoring column\\(s\\) X, region, global from .* as the column\\(s\\) ",
+                          "already exist in another mapping\\."))
     expect_identical(a, glo)
   })
 })
@@ -348,7 +350,7 @@ test_that("1on1 country mappings do not alter the data", {
 
 test_that("Bilateral aggregation works", {
   calcBilateral <- function() {
-    map <- toolGetMapping("regionmappingH12.csv")
+    map <- toolGetMapping("regionmappingH12.csv", where = "madrat")
     tmp <- expand.grid(map[[2]], map[[2]], stringsAsFactors = FALSE)
     x <- new.magpie(paste0(tmp[[1]], ".", tmp[[2]]))
     x[, , ] <- rep(seq_len(nrow(map)), nrow(map))

diff --git a/tests/testthat/test-toolGetMapping.R b/tests/testthat/test-toolGetMapping.R
@@ -38,4 +38,12 @@ test_that("toolGetMapping works", {
   writeLines("abc", paste0(getConfig("mappingfolder"), "/test.xyz"))
   expect_error(toolGetMapping("test.rda", where = "mappingfolder"), "did not contain a object")
   expect_error(toolGetMapping("test.xyz"), "Unsupported filetype")
+
+  readTest <- function() {
+    toolGetMapping("regionmappingH12.csv", type = "regional")
+    return(as.magpie(1))
+  }
+  globalassign("readTest")
+  expect_warning(readSource("Test"),
+                 "argument 'where' should be set when calling toolGetMapping from within a madrat function.")
 })