Merge pull request #1 from datashield/v1.0.0-dev

first commit

Author: timcadman

DESCRIPTION

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+Package: dsExampleClient
+Title: Provide an example of DataSHIELD Client-Side package
+Version: 1.0.0
+Authors@R: 
+    person("Tim", "Cadman", , "t.j.cadman@umcg.nl", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-7682-5645"))
+Description: A complete DataSHIELD client-side package containing one exported function as an example how to create a DataSHIELD package.
+License: LGPL (>= 3)
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
+Imports:
+    DSI,
+    cli
+Suggests: 
+    knitr,
+    rmarkdown,
+    testthat (>= 3.0.0), 
+    DSLite, 
+    devtools, 
+    dsBase
+Config/testthat/edition: 3
+VignetteBuilder: knitr

LICENSE.md

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+GNU Lesser General Public License
+=================================
+
+_Version 3, 29 June 2007_  
+_Copyright © 2007 Free Software Foundation, Inc. &lt;<http://fsf.org/>&gt;_
+
+Everyone is permitted to copy and distribute verbatim copies
+of this license document, but changing it is not allowed.
+
+
+This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+### 0. Additional Definitions
+
+As used herein, “this License” refers to version 3 of the GNU Lesser
+General Public License, and the “GNU GPL” refers to version 3 of the GNU
+General Public License.
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+“The Library” refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
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+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
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+
+### 1. Exception to Section 3 of the GNU GPL
+
+You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+### 2. Conveying Modified Versions
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+If you modify a copy of the Library, and, in your modifications, a
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+### 3. Object Code Incorporating Material from Library Header Files
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NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(ds.funLevels)
+importFrom(DSI,datashield.aggregate)
+importFrom(DSI,datashield.connections_find)
+importFrom(cli,cli_abort)

R/ds.funLevels.R

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+#' @title Returns levels of a factor variable with fun message
+#' @description Retrieves the number of columns in a dataset and provides a motivational message
+#' @param x a character string providing the name of the input data frame or matrix.
+#' @param fun_message a character string with the motivational message
+#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login.
+#' If the \code{datasources} argument is not specified
+#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
+#' @return \code{ds.funLevels} returns the levels prefixed by a fun message
+#' @author Tim Cadman
+#' @importFrom DSI datashield.aggregate datashield.connections_find
+#' @examples
+#' \dontrun{
+#' ds.funLevels(
+#'   df.name = "iris$Species",
+#'   fun_message = "This is a fun message ,",
+#'   dataources = conns
+#' )
+#' }
+#' @export
+ds.funLevels <- function(x=NULL, fun_message=NULL, datasources=NULL) {
+
+  if(is.null(datasources)){
+    datasources <- datashield.connections_find()
+  }
+
+  .check_args(x, fun_message)
+  fun_message_no_spaces <- gsub(" ", "", fun_message)
+  cally <- call("funLevelsDS", x, fun_message_no_spaces)
+  fun_levels <- DSI::datashield.aggregate(datasources, cally)
+
+  return(fun_levels)
+
+}
+
+#' Validate Arguments
+#'
+#' This function checks whether the provided arguments meet the expected conditions.
+#' It ensures that `x` and `fun_message` are not `NULL` and that both are character vectors.
+#'
+#' @param x A character vector. Must not be `NULL`.
+#' @param fun_message A character vector. Must not be `NULL`.
+#' @return This function does not return a value. It throws an error if any of the conditions are not met.
+#' @importFrom cli cli_abort
+.check_args <- function(x, fun_message) {
+
+  if(is.null(x))  {
+    cli_abort("`x` must not be NULL")
+  }
+
+  if(is.null(fun_message)) {
+      cli_abort("`fun_message` must not be NULL")
+  }
+
+  x_class <- class(x)
+  message_class <- class(fun_message)
+
+  if(x_class != "character") {
+    cli_abort(
+      c(
+        "x" = "`x` must be a character vector",
+        "i" = "You have provided an input with class {x_class}")
+    )
+  }
+
+  if(message_class != "character") {
+    cli_abort(
+      c(
+        "x" = "`fun_message` must be a character vector",
+        "i" = "You have provided an input with class {message_class}")
+    )
+  }
+
+}

README.md

@@ -1,2 +1,26 @@
+
 # dsExampleClient
-DataSHIELD Example Client
+
+The goal of dsExampleClient is to show how to write a basic DataSHIELD client-side package. 
+
+## Installation
+
+Clone this repository by opening the terminal in R and typing:
+
+```
+git clone https://github.com/timcadman/dsExample my/target/path
+```
+
+To use this package as a template for your new DataSHIELD package, perform the following steps:
+- Log in to Github and create a github repository for your new package
+- Create a local folder for your new package and copy this repository to that folder
+- Open the terminal in R, navigate to the folder of your new package and type:
+```
+git init
+```
+
+## Link this package with your new repository by typing in the terminal:
+```
+git remote add origin https://github.com/myGithubUsername/myNewPackageClient
+```
+

dsExampleClient.Rproj

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+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

man/dot-check_args.Rd

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+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(dsExampleClient)
+
+test_check("dsExampleClient")