v0.9.1

From NEWS.md file: * added descriptions of validation results and details to validate() function * added version info to package and to xml exports * added warning to enter_new_metadata() if format = TRUE as it sometimes leads to corrupt files. using format = FALSE fixes this, but the file still contains the example data. Merge branch 'dev' # Conflicts: # DESCRIPTION # Makefile # NEWS.md # R/updateFromNewSheet.R # docs/description_emescheme.html # docs/index.html # docs/r_package_introduction.html # docs/user_manual.html # source/index.Rmd # vignettes/description_emescheme.Rmd # vignettes/user_manual.Rmd
Exp-Micro-Ecol-Hub · Apr 10, 2019 · cea7a3e · cea7a3e
2 parents e4db30c + 3e0c9eb
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diff --git a/.covrignore b/.covrignore
@@ -0,0 +1 @@
+R/updateFromNewSheet.R
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
+inst/doc
 doc
 Meta
 /doc

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,31 +1,28 @@
 Package: emeScheme
-Title: Microcosm experiment metadata scheme
-Version: 0.9
-Date: 2019-04-01
-Authors@R: c( person( "Rainer M.", "Krug", role = c("aut", "cre"),
-        email = "Rainer.Krug@uzh.ch" ), person( "Owen L.", "Petchey",
-        role = c("ctb"), email = "Owen.Petchey@uzh.ch" ),
-        person("Vanessa W.", "de Melo", role = c("ctb"), email =
-        "Vanessa Weber de Melo <vanessa.weberdemelo@uzh.ch>" ),
-        person("Frank", "Pennekamp", role = c("ctb"), email = "Frank
-        Pennekamp <frank.pennekamp@uzh.ch>") )
-Description: This package provides and describes the Authoratative
-        definition of th emeScheme (Experimental Microcosm Ecology
-        Metadata). ---- Data imported and version bumped at Tue Mar 19
-        12:00:41 2019 / Europe/Zurich.
+Title: Microcosm Experiment Metadata Scheme
+Description: The Authoratative definition of the emeScheme (Experimental Microcosm Ecology Metadata) and tools to enter, validate and export the metadata.
+                 ---- Data updated and version bumped at Wed Apr 10 08:53:29 2019 / Europe/Zurich. ---- Data updated and version bumped at Wed Apr 10
+                 10:51:12 2019 / Europe/Zurich.
+Version: 0.9.1
+emeSchemeVersion: 0.9.5
+Date: 2019-04-10
+Authors@R: c( person( "Rainer M.", "Krug", role = c("aut", "cre"), email = "Rainer.Krug@uzh.ch" ), person( "Owen L.", "Petchey", role = c("ctb"), email =
+                 "Owen.Petchey@uzh.ch" ), person("Vanessa W.", "de Melo", role = c("ctb"), email = "Vanessa Weber de Melo <vanessa.weberdemelo@uzh.ch>" ),
+                 person("Frank", "Pennekamp", role = c("ctb"), email = "Frank Pennekamp <frank.pennekamp@uzh.ch>") )
+URL: https://exp-micro-ecol-hub.github.io/emeScheme/, https://github.com/Exp-Micro-Ecol-Hub/emeScheme
+BugReports: https://github.com/Exp-Micro-Ecol-Hub/emeScheme/issues
+DOI: https://zenodo.org/record/2620097
 Depends: R (>= 3.3.0)
-Imports: tools, methods, utils, magrittr (>= 1.5), dplyr (>= 0.1.8),
-        tibble (>= 2.1.1), readxl (>= 1.2.0), openxlsx (>= 4.1.1), XML
-        (>= 3.98-1.16), rlang (>= 0.3.1), taxize (>= 0.9.5), rmarkdown,
-        knitr, digest (>= 0.6)
+Imports: tools, methods, utils, magrittr (>= 1.5), dplyr (>= 0.1.8), tibble (>= 2.1.1), readxl (>= 1.2.0), openxlsx (>= 4.1.1), XML (>= 3.98-1.16), rlang (>=
+                 0.3.1), taxize (>= 0.9.5), rmarkdown, knitr, digest (>= 0.6)
 Remotes: awalker89/openxlsx, rkrug/plantuml
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 StagedInstall: true
 RoxygenNote: 6.1.1
-Suggests: covr (>= 3.2.1), testthat (>= 2.0.1), googlesheets (>=
-        0.3.0), here (>= 0.1), kableExtra (>= 0.9.0), plantuml (>=
-        0.2.3.2)
-GSUpdate: 2019-03-18 13:39:12
+Suggests: covr (>= 3.2.1), testthat (>= 2.0.1), here (>= 0.1), kableExtra (>= 0.9.0)
+Enhances: plantuml (>= 0.2.3.2)
+emeSchemeUpdate: 2019-04-10 10:51:12
+emeSchemeMD5: 7115b9352958a51fcb60e484a8b9754d
 VignetteBuilder: knitr
diff --git a/Makefile b/Makefile
@@ -1,7 +1,7 @@
 ## R parts based on https://github.com/yihui/knitr/blob/master/Makefile
 
-PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
-PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
+PKGNAME := $(shell sed -n "s/^Package: *\([^ ]*\)/\1/p" DESCRIPTION)
+PKGVERS := $(shell sed -n "s/^Version: *\([^ ]*\)/\1/p" DESCRIPTION)
 PKGSRC  := $(shell basename `pwd`)
 
 
@@ -132,38 +132,26 @@ test:
 
 ####
 
-############# mHelp targets #############
+############# Help targets #############
 
-list_files:
-	@echo PKGNAME : $(PKGNAME)
-	@echo PKGVERS : $(PKGVERS)
-	@echo PKGSRC  : $(PKGSRC)
+list_variables:
 	@echo
-	@echo SRCDIR  : $(SRCDIR)
-	@echo OUTDIR  : $(OUTDIR)
-	@echo DATADIR : $(DATADIR)
-	@echo
-	@echo VIGDIR  : $(VIGDIR)
-	@echo VIGHTMLDIR  : $(VIGHTMLDIR)
-	@echo
-	@echo READMERMD : $(READMERMD)
-	@echo READMEMD : $(READMEMD)
-	@echo
-	@echo VIGRMD  : $(VIGRMD)
-	@echo TMP1    : $(TMP1)
-	@echo VIGHTML : $(VIGHTML)
-	@echo VIGHTMLOUT : $(VIGHTMLOUT)
-	@echo
-	@echo RMD     : $(RMD)
-	@echo TMP2    : $(TMP2)
-	@echo HTML    : $(HTML)
-	@echo
-	@echo EXAMPLEXML : $(EXAMPLEXML)
+	@echo "#############################################"
+	@echo "## Variables ################################"
+	make -pn | grep -A1 "^# makefile"| grep -v "^#\|^--" | sort | uniq
+	@echo "#############################################"
+	@echo ""
 
 ## from https://stackoverflow.com/a/26339924/632423
-list: list_files
+list_targets:
 	@echo
+	@echo "#############################################"
+	@echo "## Targets    ###############################"
 	@$(MAKE) -pRrq -f $(lastword $(MAKEFILE_LIST)) : 2>/dev/null | awk -v RS= -F: '/^# File/,/^# Finished Make data base/ {if ($$1 !~ "^[#.]") {print $$1}}' | sort | egrep -v -e '^[^[:alnum:]]' -e '^$@$$'
+	@echo "#############################################"
+	@echo
+
+list: list_variables list_targets
 
 #############
 

diff --git a/NAMESPACE b/NAMESPACE
@@ -11,6 +11,7 @@ S3method(print,emeScheme_validation)
 export(as.plantuml.emeSchemeData)
 export(as.plantuml.emeSchemeSet)
 export(emeSchemeToXml)
+export(emeSchemeVersions)
 export(emeScheme_extract)
 export(emeScheme_split)
 export(enter_new_metadata)
@@ -36,6 +37,7 @@ importFrom(knitr,purl)
 importFrom(magrittr,"%<>%")
 importFrom(magrittr,"%>%")
 importFrom(magrittr,equals)
+importFrom(magrittr,extract)
 importFrom(magrittr,extract2)
 importFrom(magrittr,not)
 importFrom(magrittr,set_names)
@@ -51,7 +53,9 @@ importFrom(tibble,is_tibble)
 importFrom(tibble,tibble)
 importFrom(tools,file_ext)
 importFrom(tools,file_path_sans_ext)
+importFrom(tools,md5sum)
 importFrom(utils,RShowDoc)
 importFrom(utils,URLencode)
 importFrom(utils,browseURL)
+importFrom(utils,packageDescription)
 importFrom(utils,read.csv)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# release 0.9.1
+**emeScheme version 0.9.5**
+* added descriptions of validation results and details to validate() function
+* added version info to package and to xml exports
+* added warning to enter_new_metadata() if format = TRUE as it sometimes leads to corrupt files. using format = FALSE fixes this, but the file still contains the example data.
+
 # release 0.9
 This should finalise the spreadsheet
 

diff --git a/R/data.emeScheme_example.R b/R/data.emeScheme_example.R
@@ -1,7 +1,6 @@
 #' emeScheme_example as imported from the Google sheet.
 #'
 #' The dataset contains example data. It was created by using the code below.
-#' @source \url{https://docs.google.com/spreadsheets/d/1OAyRM1jGL5Vho-YfPffePhwGpQtaBUeTPJV6P98f0Bc}
 #'
 #' @examples
 #' \dontrun{

diff --git a/R/data.emeScheme_raw.R b/R/data.emeScheme_raw.R
@@ -1,12 +1,11 @@
 #' emeScheme_raw as imported from the Google sheet.
 #'
 #' The dataset contains raw data. It was created by using the code below.
-#' @source \url{https://docs.google.com/spreadsheets/d/1OAyRM1jGL5Vho-YfPffePhwGpQtaBUeTPJV6P98f0Bc}
 #'
 #' @examples
 #' \dontrun{
 #' ## Created by using
-#' path <- system.fil;e( "googlesheet", "emeScheme.xlsx", package = "emeScheme")
+#' path <- system.fil;e( "emeScheme.xlsx", package = "emeScheme")
 #' emeScheme_raw <- read_from_excel(
 #'   file = path,
 #'   keepData = FALSE,

diff --git a/R/emeSchemeToXml.emeSchemeSet.R b/R/emeSchemeToXml.emeSchemeSet.R
@@ -28,9 +28,16 @@ emeSchemeToXml.emeSchemeSet <- function(
 
   ## x is of type emeSchemeSet and contains therefore child nodes -------------------------
 
-  xml <- XML::xmlNode(tag)
+  xml <- XML::xmlNode("emeSchemeVersion", attrs = attr(x, "emeSchemeVersion"))
 
-# Add attributes if output == complete ------------------------------------
+# Add emeSchemeVersion ----------------------------------------------------
+
+  xml <- XML::append.xmlNode(
+    xml,
+    XML::xmlNode(tag)
+  )
+
+  # Add attributes if output == complete ------------------------------------
 
   if (output == "complete") {
     XML::xmlAttrs(

diff --git a/R/emeSchemeVersions.R b/R/emeSchemeVersions.R
@@ -0,0 +1,36 @@
+#' Returns versions of package and emeScheme
+#'
+#' @param lib.loc a character vector of directory names of R libraries, or NULL.
+#'   The default value of NULL corresponds to all libraries currently known. If
+#'   the default is used, the loaded packages and namespaces are searched before
+#'   the libraries.
+#'
+#' @return a named \code{list()}, containing the following objects:
+#' \itemize{
+#'   \item{package}{ containing an object of length on of type \code{package_version} with the version of the package}
+#'   \item{emeScheme}{ containing an object of length on of type \code{numeric_version} with the version of the metadata scheme emeScheme}
+#' }
+#'
+#' @importFrom utils packageDescription
+#' @export
+#'
+#' @examples
+#' emeSchemeVersions()
+emeSchemeVersions <-function (
+  lib.loc = NULL
+)
+{
+  pkg = "emeScheme"
+  res <- suppressWarnings(
+    packageDescription(
+      pkg,
+      lib.loc = lib.loc,
+      fields = c( "Version", "emeSchemeVersion")
+    )
+  )
+  res <- list(
+    package = package_version(res$Version),
+    emeScheme = numeric_version(res$emeSchemeVersion)
+  )
+  return(res)
+}
diff --git a/R/enter_new_metadata.R b/R/enter_new_metadata.R
@@ -1,14 +1,13 @@
 #' Enter new metadata to fill a new scheme
 #'
-#' Open \code{emeScheme.xlsx} from system.file("googlesheet",
-#' "emeScheme.xlsx", package = "emeScheme") in excel. New data can be entered
-#' and the file has to be saved at a different location as it is a read-only
-#' file.
+#' Open \code{system.file("emeScheme.xlsx", package = "emeScheme")} in excel.
+#' New data can be entered and the file has to be saved at a different location
+#' as it is a read-only file.
 #'
 #' @param file if not \code{NULL}, the te,plate will be saved to this file.
 #' @param open if \code{TRUE}, the file will be opened. This can produce different results depending on the OS, browsr and browser settings.
 #' @param keepData if \code{TRUE} the data entry areas will be emptied. If \code{FALSE}. the example data will be included.
-#' @param format if \code{FALSE} the sheet will be opened as the googledoc sheet formated is. if \code{TRUE}, it will be formated nicely.
+#' @param format if \code{FALSE} the sheet will be opened as the sheet is. if \code{TRUE}, it will be formated nicely.
 #' @param overwrite if \code{TRUE}, the file specified in \code{file} will be overwritten. if \code{FALSE}, an error will be raised ehen the file exists.
 #' @param verbose if \code{TRUE} print usefull information
 #' @param .skipBrowseURL internal use (testing only). if \code{TRUE} skip the call of \code{browseURL()}
@@ -52,20 +51,44 @@ enter_new_metadata <- function(
     }
   )
   ##
-  fn <- file.path( tempdir(), "emeScheme.xlsx")
+
+# Warning if `format = TRUE` ----------------------------------------------
+  if (format) {
+    warning(
+    "The argument `format` is set to TRUE (the default).\n",
+    "Corruptions of the formated xlsx filer were recently observed!.\n",
+    "\n",
+    "If the resulting xlsx file is corrupt, please use\n",
+    "\n",
+    "`format = FALSE`",
+    "\n",
+    "when calling `enter_new_metadata()`\n",
+    "\n",
+    "This does NOT delete the example data.\n"
+    )
+  }
+
+# Temporary file name -----------------------------------------------------
+
+  fn <- tempfile(pattern = "emeScheme.", fileext = ".xlsx")
+
+# Format if asked for, otherwise copy to fn unchanged ---------------------
+
   if (format) {
     format_emeScheme_xlsx(
-      fn_org = system.file("googlesheet", "emeScheme.xlsx", package = "emeScheme"),
+      fn_org = system.file("emeScheme.xlsx", package = "emeScheme"),
       fn_new = fn,
       keepData = keepData
     )
   } else {
     file.copy(
-      from = system.file("googlesheet", "emeScheme.xlsx", package = "emeScheme"),
+      from = system.file("emeScheme.xlsx", package = "emeScheme"),
       to = fn
     )
   }
 
+# If file specified, copy temporary file to final destination -------------
+
   if (!is.null(file)) {
     result <- file.copy(
       from = fn,
@@ -86,7 +109,9 @@ enter_new_metadata <- function(
       cat_ln()
     }
   }
-  ##
+
+# If open == TRUE, open the file ------------------------------------------
+
   if (open) {
     if (verbose) {
       cat_ln("Trying to open the file by opening it in the browser'", fn, "'... ")
@@ -97,7 +122,9 @@ enter_new_metadata <- function(
       utils::browseURL(fn)
     }
   }
-  ##
+
+# Return invisibly the final file name ------------------------------------
+
   invisible(fn)
 }
 
diff --git a/R/format_emeScheme_xlsx.R b/R/format_emeScheme_xlsx.R
@@ -1,6 +1,7 @@
-#' Format the \code{googlesheet/emeScheme.xlsx}
+#' Format the file \code{system.file("emeScheme.xlsx", package = "emeScheme")}
 #'
-#' Takes no arguments. Loads  \code{system.file("googlesheet", "emeScheme.xlsx", package = "emeScheme")}, formats it and saves it under the same name.
+#' Takes no arguments. Loads  \code{system.file("emeScheme.xlsx", package =
+#' "emeScheme")}, formats it and saves it under the same name.
 #' @param fn_org file name of the original excel file to be formated
 #' @param fn_new file name where the final xlsx should be saved to. If missing, it will not be saved.
 #' @param keepData if \code{TRUE}, data from data cells will be empty
@@ -160,7 +161,7 @@ format_emeScheme_xlsx <- function(
     rowNames <- unlist(data[,nameCol])
 
     dataRows <- 2:nrow(data)
-    dataCols <- which(colNames == "DATA"):ncol(data)
+    dataCols <- grep("DATA", colNames):ncol(data)
 
     # format data range -------------------------------------------------------
 
@@ -255,7 +256,7 @@ format_emeScheme_xlsx <- function(
     colNames <- unlist(data[nameRow,])
 
     dataCols <- 2:ncol(data)
-    dataRows <- which(rowNames == "DATA"):nrow(data)
+    dataRows <- grep("DATA", rowNames):nrow(data)
 
     # format data range -------------------------------------------------------
 

diff --git a/R/make_example.R b/R/make_example.R
@@ -38,7 +38,7 @@ make_example <- function(
     )
     if (name == "basic") {
       format_emeScheme_xlsx(
-        fn_org = system.file("googlesheet", "emeScheme.xlsx", package = "emeScheme"),
+        fn_org = system.file("emeScheme.xlsx", package = "emeScheme"),
         fn_new = file.path(".", name, "expt1_emeScheme.xlsx"),
         keepData = TRUE
       )

diff --git a/R/new_emeSchemeData.R b/R/new_emeSchemeData.R
@@ -79,7 +79,7 @@ new_emeSchemeData <- function(
 # extract attributes to set -----------------------------------------------
 
   attrToSet <- x$valueProperty
-  attrToSet <- attrToSet[1:(which(x$valueProperty == "DATA")-1)]
+  attrToSet <- attrToSet[1:(grep("DATA", x$valueProperty)-1)]
 
 # set attributes ----------------------------------------------------------
 

diff --git a/R/new_emeSchemeSet.R b/R/new_emeSchemeSet.R
@@ -55,6 +55,10 @@ attr(result, "propertyName") <- attr(x, "fileName")
     class(result),
   )
 
+  # Set emeSchemeVersion attribute-------------------------------------------
+
+  attr(result, "emeSchemeVersion") <- attr(x, "emeSchemeVersion")
+
 # Return ------------------------------------------------------------------
 
   return(result)
-Original file line number
+Diff line change
@@ -1,3 +1,4 @@
+    inst/doc
     doc
     Meta
     /doc
@@ Expand Down @@