Completed working test suite and added CI

R/.Rbuildignore

@@ -1,2 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.travis\.yml$
+^appveyor\.yml$

R/.travis.yml

@@ -0,0 +1,5 @@
+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
+
+language: R
+sudo: false
+cache: packages

R/appveyor.yml

@@ -0,0 +1,45 @@
+# DO NOT CHANGE the "init" and "install" sections below
+
+# Download script file from GitHub
+init:
+  ps: |
+        $ErrorActionPreference = "Stop"
+        Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
+        Import-Module '..\appveyor-tool.ps1'
+
+install:
+  ps: Bootstrap
+
+cache:
+  - C:\RLibrary
+
+# Adapt as necessary starting from here
+
+build_script:
+  - travis-tool.sh install_deps
+
+test_script:
+  - travis-tool.sh run_tests
+
+on_failure:
+  - 7z a failure.zip *.Rcheck\*
+  - appveyor PushArtifact failure.zip
+
+artifacts:
+  - path: '*.Rcheck\**\*.log'
+    name: Logs
+
+  - path: '*.Rcheck\**\*.out'
+    name: Logs
+
+  - path: '*.Rcheck\**\*.fail'
+    name: Logs
+
+  - path: '*.Rcheck\**\*.Rout'
+    name: Logs
+
+  - path: '\*_*.tar.gz'
+    name: Bits
+
+  - path: '\*_*.zip'
+    name: Bits

R/tests/testthat/data/create-ref-data.R

@@ -1,3 +1,49 @@
+# Setup -------------------------------------------------------------------
+
+devtools::load_all()
+
+library(digest)
+library(magrittr)
+library(jsonlite)
+
+
+ref_data_location <- function(x) file.path("tests","testthat","data", x)
+
+# RCurl -------------------------------------------------------------------
+
+REDCap_split(
+  ref_data_location("ExampleProject_records.json") %>% fromJSON,
+  ref_data_location("ExampleProject_metadata.json") %>% fromJSON
+  ) %>% digest
+
+
+# Basic CSV ---------------------------------------------------------------
+
+REDCap_split(
+  ref_data_location("ExampleProject_DATA_2018-06-07_1129.csv") %>% read.csv,
+  ref_data_location("ExampleProject_DataDictionary_2018-06-07.csv") %>% read.csv
+  ) %>% digest
+
+# REDCap R Export ---------------------------------------------------------
+
+source("tests/testthat/helper-ExampleProject_R_2018-06-07_1129.r")
+
+REDCap_split(
+  ref_data_location("ExampleProject_DATA_2018-06-07_1129.csv") %>%
+    read.csv %>%
+    REDCap_process_csv,
+  ref_data_location("ExampleProject_DataDictionary_2018-06-07.csv") %>% read.csv
+  ) %>% digest
+
 # Longitudinal data from @pbchase; Issue #7 -------------------------------
 
-# Something will go here.
+file_paths <- sapply(
+  c(
+    records = "WARRIORtestForSoftwa_DATA_2018-06-21_1431.csv",
+    metadata = "WARRIORtestForSoftwareUpgrades_DataDictionary_2018-06-21.csv"
+  ), ref_data_location
+)
+
+redcap <- lapply(file_paths, read.csv, stringsAsFactors = FALSE)
+redcap[["metadata"]] <- with(redcap, metadata[metadata[,1] > "",])
+with(redcap, REDCap_split(records, metadata)) %>% digest

R/tests/testthat/helper-ExampleProject_R_2018-06-07_1129.r

@@ -1,36 +1,37 @@
 REDCap_process_csv <- function(data) {
   #Load Hmisc library
-  if (!require(Hmisc))
+  if (!requireNamespace("Hmisc", quietly = TRUE)) {
     stop("This test requires the 'Hmisc' package")
+  }
 
-  label(data$row)="Name"
-  label(data$redcap_repeat_instrument)="Repeat Instrument"
-  label(data$redcap_repeat_instance)="Repeat Instance"
-  label(data$mpg)="Miles/(US) gallon"
-  label(data$cyl)="Number of cylinders"
-  label(data$disp)="Displacement"
-  label(data$hp)="Gross horsepower"
-  label(data$drat)="Rear axle ratio"
-  label(data$wt)="Weight"
-  label(data$qsec)="1/4 mile time"
-  label(data$vs)="V engine?"
-  label(data$am)="Transmission"
-  label(data$gear)="Number of forward gears"
-  label(data$carb)="Number of carburetors"
-  label(data$color_available___red)="Colors Available (choice=Red)"
-  label(data$color_available___green)="Colors Available (choice=Green)"
-  label(data$color_available___blue)="Colors Available (choice=Blue)"
-  label(data$color_available___black)="Colors Available (choice=Black)"
-  label(data$motor_trend_cars_complete)="Complete?"
-  label(data$letter_group___a)="Which group? (choice=A)"
-  label(data$letter_group___b)="Which group? (choice=B)"
-  label(data$letter_group___c)="Which group? (choice=C)"
-  label(data$choice)="Choose one"
-  label(data$grouping_complete)="Complete?"
-  label(data$price)="Sale price"
-  label(data$color)="Color"
-  label(data$customer)="Customer Name"
-  label(data$sale_complete)="Complete?"
+  Hmisc::label(data$row)="Name"
+  Hmisc::label(data$redcap_repeat_instrument)="Repeat Instrument"
+  Hmisc::label(data$redcap_repeat_instance)="Repeat Instance"
+  Hmisc::label(data$mpg)="Miles/(US) gallon"
+  Hmisc::label(data$cyl)="Number of cylinders"
+  Hmisc::label(data$disp)="Displacement"
+  Hmisc::label(data$hp)="Gross horsepower"
+  Hmisc::label(data$drat)="Rear axle ratio"
+  Hmisc::label(data$wt)="Weight"
+  Hmisc::label(data$qsec)="1/4 mile time"
+  Hmisc::label(data$vs)="V engine?"
+  Hmisc::label(data$am)="Transmission"
+  Hmisc::label(data$gear)="Number of forward gears"
+  Hmisc::label(data$carb)="Number of carburetors"
+  Hmisc::label(data$color_available___red)="Colors Available (choice=Red)"
+  Hmisc::label(data$color_available___green)="Colors Available (choice=Green)"
+  Hmisc::label(data$color_available___blue)="Colors Available (choice=Blue)"
+  Hmisc::label(data$color_available___black)="Colors Available (choice=Black)"
+  Hmisc::label(data$motor_trend_cars_complete)="Complete?"
+  Hmisc::label(data$letter_group___a)="Which group? (choice=A)"
+  Hmisc::label(data$letter_group___b)="Which group? (choice=B)"
+  Hmisc::label(data$letter_group___c)="Which group? (choice=C)"
+  Hmisc::label(data$choice)="Choose one"
+  Hmisc::label(data$grouping_complete)="Complete?"
+  Hmisc::label(data$price)="Sale price"
+  Hmisc::label(data$color)="Color"
+  Hmisc::label(data$customer)="Customer Name"
+  Hmisc::label(data$sale_complete)="Complete?"
   #Setting Units
 
 

R/tests/testthat/helper-paths.R

@@ -0,0 +1,9 @@
+# get_data_location <- function(x) {
+#   system.file(
+#     "testdata",
+#     x,
+#     package = "REDCapRITS"
+#   )
+# }
+
+get_data_location <- function(x) file.path("data", x)

R/tests/testthat/test-API.R

@@ -1,22 +1,16 @@
 context("Reading in JSON")
 
-# Set up the path ----------------------------------------------------------
-
-data_dir <- system.file("tests", "testthat", "data", package = "REDCapRITS")
-
 # Check the RCurl export ---------------------------------------------------
 test_that("JSON character vector from RCurl matches reference", {
 
   metadata <- jsonlite::fromJSON(
-    file.path(
-      data_dir,
+    get_data_location(
       "ExampleProject_metadata.json"
     )
   )
 
   records <- jsonlite::fromJSON(
-    file.path(
-      data_dir,
+    get_data_location(
       "ExampleProject_records.json"
     )
   )

R/tests/testthat/test-csv-exports.R

@@ -1,19 +1,14 @@
 context("CSV Exports")
 
 # Set up the path and data -------------------------------------------------
-
-data_dir <- system.file("tests", "testthat", "data", package = "REDCapRITS")
-
 metadata <- read.csv(
-  file.path(
-    data_dir,
+  get_data_location(
     "ExampleProject_DataDictionary_2018-06-07.csv"
   )
 )
 
 records <- read.csv(
-  file.path(
-    data_dir,
+  get_data_location(
     "ExampleProject_DATA_2018-06-07_1129.csv"
   )
 )
@@ -26,10 +21,11 @@ test_that("CSV export matches reference", {
 })
 
 # Test that R code enhanced CSV export matches reference --------------------
-test_that("R code enhanced export matches reference", {
-  source(file.path(data_dir, "ExampleProject_R_2018-06-07_1129.r"))
+if (requireNamespace("Hmisc", quietly = TRUE)) {
+  test_that("R code enhanced export matches reference", {
+      redcap_output_csv2 <- REDCap_split(REDCap_process_csv(records), metadata)
 
-  redcap_output_csv2 <- REDCap_split(REDCap_process_csv(records), metadata)
+      expect_known_hash(redcap_output_csv2, "34f82cab35bf8aae47d08cd96f743e6b")
+  })
+}
 
-  expect_known_hash(redcap_output_csv2, "34f82cab35bf8aae47d08cd96f743e6b")
-})

R/tests/testthat/test-longitudinal.R

@@ -1,17 +1,14 @@
 context("Longitudinal data")
 
 test_that("CSV export matches reference", {
-  # Reading in the files
-  file_paths <- file.path(
-    system.file("tests", "testthat", "data", package = "REDCapRITS"),
+  file_paths <- sapply(
     c(
       records = "WARRIORtestForSoftwa_DATA_2018-06-21_1431.csv",
       metadata = "WARRIORtestForSoftwareUpgrades_DataDictionary_2018-06-21.csv"
-    )
+    ), get_data_location
   )
 
   redcap <- lapply(file_paths, read.csv, stringsAsFactors = FALSE)
-  names(redcap) <- c("records", "metadata")
   redcap[["metadata"]] <- with(redcap, metadata[metadata[,1] > "",])
   redcap_output <- with(redcap, REDCap_split(records, metadata))
 

README.md

@@ -157,6 +157,9 @@ welcome your contributions!
 ## Instructions
 ### R
 
+[![Travis-CI Build Status](https://travis-ci.org/SpectrumHealthResearch/REDCapRITS.svg?branch=master)](https://travis-ci.org/SpectrumHealthResearch/REDCapRITS)
+[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/SpectrumHealthResearch/REDCapRITS?branch=master&svg=true)](https://ci.appveyor.com/project/SpectrumHealthResearch/REDCapRITS)
+
 #### Installation
 
 First you must install the package. To do so, execute the following in your R console: