Merge pull request #320 from vimc/mrc-3665

mrc-3665 way for orderly web to control demo data

Author: hillalex

.gitignore

@@ -13,3 +13,6 @@ tests/testthat/montagu-reports
 tests/testthat/reference/*.zip
 orderly_*.tar.gz
 tests/testthat/tmp
+/doc/
+/Meta/
+.idea

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: orderly
 Title: Lightweight Reproducible Reporting
-Version: 1.4.10
+Version: 1.5.0
 Description: Order, create and store reports from R.  By defining a
     lightweight interface around the inputs and outputs of an
     analysis, a lot of the repetitive work for reproducible research
@@ -46,7 +46,7 @@ Suggests:
     rmarkdown,
     testthat,
     vaultr (>= 1.0.4)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
 Language: en-GB

NEWS.md

@@ -1,3 +1,8 @@
+# orderly 1.5.0
+
+* Add `prepare_git_example_from_source` which can be used to generate a git controlled orderly directory
+from a source, and another entrypoint `run_orderly_demo` that exposes this function, for use in testing OrderlyWeb (mrc-3665)
+
 # orderly 1.4.7
 
 * Add `orderly_cancel_remote` which can be used to cancel one or more reports running on a remote via its key (mrc-3167)

R/testing.R

@@ -51,6 +51,19 @@ create_orderly_demo <- function(path = tempfile(), quiet = FALSE,
 }
 
 
+prepare_git_example_from_source <- function(source_path, path) {
+  temp <- file.path(tempfile(), "demo")
+  fs::dir_copy(source_path, temp)
+  generate_source_db(temp)
+  run_orderly_demo(temp)
+  build_git_demo(temp)
+  res <- prepare_orderly_git_example(path, run_report = FALSE)
+  options(orderly.server.demo = NULL)
+  unlink(temp, recursive = TRUE)
+  res
+}
+
+
 run_orderly_demo <- function(path, quiet = FALSE) {
   if (quiet) {
     oo <- options(orderly.nolog = TRUE)
@@ -79,6 +92,7 @@ run_orderly_demo <- function(path, quiet = FALSE) {
   path
 }
 
+
 ## This is a really rubbish set of test data.  It requires an open
 ## "source" database and will write out two tables.  This is used by
 ## the examples.
@@ -115,6 +129,17 @@ prepare_orderly_example <- function(name, path = tempfile(), testing = FALSE,
   src_files <- dir(src, full.names = TRUE)
   file_copy(src_files, path, overwrite = TRUE, recursive = TRUE)
 
+  generate_source_db(path)
+
+  if (git) {
+    prepare_basic_git(path, quiet = TRUE)
+  }
+
+  path
+}
+
+
+generate_source_db <- function(path) {
   if (file.exists(file.path(path, "source.R"))) {
     generator <- source(file.path(path, "source.R"), local = TRUE)$value
   } else {
@@ -125,12 +150,6 @@ prepare_orderly_example <- function(name, path = tempfile(), testing = FALSE,
   if (length(con) > 0L) {
     generator(con)
   }
-
-  if (git) {
-    prepare_basic_git(path, quiet = TRUE)
-  }
-
-  path
 }
 
 
@@ -196,8 +215,10 @@ demo_change_time <- function(id, time, path) {
 ## extendable...
 ##
 ## After building this we have two branches 'master' with
-build_git_demo <- function() {
-  path <- prepare_orderly_example("demo", file.path(tempfile(), "demo"))
+build_git_demo <- function(path = NULL) {
+  if (is.null(path)) {
+    path <- prepare_orderly_example("demo", file.path(tempfile(), "demo"))
+  }
   dir.create(file.path(path, "extra"))
   move <- setdiff(dir(file.path(path, "src"), pattern = "^[^.]+$"),
                   c("minimal", "global"))

docker/Dockerfile

@@ -53,6 +53,7 @@ COPY . /orderly
 RUN R CMD INSTALL /orderly && \
   Rscript -e 'orderly:::write_script("/usr/bin")' && \
   cp /orderly/inst/create_orderly_demo.sh /usr/bin/ && \
+  cp /orderly/inst/run_orderly_demo /usr/bin/ && \
   rm -rf /orderly
 
 ENTRYPOINT ["/usr/bin/orderly"]

docker/teamcity-demo.sh

@@ -0,0 +1,9 @@
+#!/bin/sh
+set -ex
+if [ "$#" -ne 2 ]; then
+    echo "Expected two arguments (source_path, dest_path)"
+    exit 1
+fi
+SRC=$1
+DEST=$2
+Rscript -e "orderly:::prepare_git_example_from_source(\"$SRC\", \"$DEST\")"

inst/run_orderly_demo

@@ -16,3 +16,16 @@ test_that("create_orderly_demo can create a git repo", {
   expect_true(file.exists(file.path(path, ".git")))
   expect_true(same_path(gert::git_pull(repo = path), path))
 })
+
+
+test_that("can create an orderly git repo from given source", {
+  skip_on_cran()
+  path <- tempfile()
+  dir.create(path)
+  on.exit(unlink(path, recursive = TRUE))
+  source <- system.file("examples/demo", package = "orderly")
+  prepare_git_example_from_source(source, path)
+  expect_true(file.exists(file.path(path, ".git")))
+  expect_true(dir.exists(file.path(path, "archive")))
+  expect_true(same_path(gert::git_pull(repo = path), path))
+})