Added insertStructure() and subfunctions

.github/workflows/R-CMD-check.yaml

@@ -37,6 +37,32 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
 
+      - name: Install Linux system libraries
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            libcairo2-dev \
+            libfribidi-dev \
+            libfontconfig1-dev \
+            libfreetype6-dev \
+            libharfbuzz-dev \
+            libjpeg-dev \
+            libpng-dev \
+            libtiff5-dev \
+            libwebp-dev \
+            pkg-config
+
+      - name: Configure Linux Makevars for gdtools
+        if: runner.os == 'Linux'
+        run: |
+          mkdir -p ~/.R
+          cat <<EOF >> ~/.R/Makevars
+          CPPFLAGS=$(pkg-config --cflags cairo freetype2 fontconfig)
+          LDFLAGS=$(pkg-config --libs-only-L cairo freetype2 fontconfig)
+          LDLIBS=$(pkg-config --libs-only-l cairo freetype2 fontconfig)
+          EOF
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck

DESCRIPTION

@@ -29,7 +29,8 @@ Imports:
     stringr,
     zip,
     here,
-    fs
+    fs,
+    usethis
 Config/roxygen2/version: 8.0.0
 Suggests: 
     testthat (>= 3.0.0)

NAMESPACE

@@ -4,6 +4,7 @@ export(arrangeCdmNames)
 export(assertCdmNames)
 export(createResultsDir)
 export(getPkgZips)
+export(insertStructure)
 export(setLoggers)
 export(unZipStudyFiles)
 export(zipStudyFiles)

R/insertStructure.R

@@ -0,0 +1,230 @@
+#' Install default package bundle
+#'
+#' Installs a predefined set of DARWIN EU®/OHDSI packages into the study project
+#' and updates their dependencies. The standard package list includes the packages
+#' omopgenerics, PhenotypeR, DrugExposureDiagnostics, CohortConstructor,
+#' IncidencePrevalence, DrugUtilisation, CohortCharacteristics, CohortSurvival,
+#' visOmopResults and DarwinShinyModules.
+#'
+#' @return
+#' An invisible list of the installed packages.
+installPackageBundle <- function(path) {
+
+  # Install default package bundle
+  complete_darwin <- list(
+    cran = c(
+      "omopgenerics",
+      "PhenotypeR",
+      "DrugExposureDiagnostics",
+      "CohortConstructor",
+      "IncidencePrevalence",
+      "DrugUtilisation",
+      "CohortCharacteristics",
+      "CohortSurvival",
+      "visOmopResults"
+    ),
+    github = c(
+      "darwin-eu/DarwinShinyModules"
+    )
+  )
+
+  if (!dir.exists(file.path(path, "renv"))) {
+    cli::cli_abort(
+      message = c(
+        "x" = "No renv detected in {.path {path}}.",
+        "i" = "Need to initialize the environment with {.fn renv::init} first."
+      )
+    )
+  }
+
+  # withr::with_dir(path, {
+    # Install packages with renv
+    renv::install(
+      packages = complete_darwin$cran, 
+      project = path
+    )
+    renv::install(
+      packages = complete_darwin$github,
+      project = path
+    )
+
+    # Add dependencies (default type = "Imports")
+    pkg_names <- c(
+      complete_darwin$cran,
+      basename(complete_darwin$github)
+    )
+
+    if (!requireNamespace("usethis", quietly = TRUE)) {
+      cli::cli_inform(
+        "Installing required package: 'usethis'"
+      )
+      renv::install(
+        packages = "usethis",
+        project = path
+      )
+    }
+
+    for (pkg in pkg_names) {
+      usethis::use_package(pkg)
+    }
+
+    # Update lockfile
+    renv::snapshot(
+      project = path
+    )
+  # })
+
+  # Return invisible package list
+  invisible(pkg_names)
+
+}
+
+
+#' Insert default documentation files
+#'
+#' Creates default `NEWS.md`, `README.Rmd` and `LICENSE.md` (Apache License 2.0) files.
+#'
+#' @return
+#' No return value.
+insertDocs <- function(path) {
+  withr::with_dir(path, {
+    usethis::use_news_md(open = FALSE)
+    usethis::use_readme_rmd(open = FALSE)
+    usethis::use_apl2_license()
+  })
+}
+
+
+#' Insert default study files
+#'
+#' Creates the `inst` and `extras` folders and populates the `R` folder with
+#' ready files for standard study functions.
+#'
+#' @param path Character string identifying the path to the study project,
+#' default `"."`.
+#' @param n_obj Number of study objectives, default `n_obj = 3`.
+#'
+#' @return
+#' No return value.
+insertStudyFiles <- function(
+    path = ".",
+    n_obj = 3
+    ) {
+  # R/
+  if ("hello.R" %in% list.files(file.path(path, "R"))) {
+    unlink(file.path(path, "R/hello.R"))
+  }
+  usethis::use_r("createCohorts", open = FALSE)
+  usethis::use_r("runStudy", open = FALSE)
+  usethis::use_r("runDiagnostics", open = FALSE)
+  usethis::use_r("pullFromAtlas", open = FALSE)
+  usethis::use_r("utils", open = FALSE)
+  usethis::use_r("globals", open = FALSE)
+  usethis::use_r("merge", open = FALSE)
+  for (i in 1:n_obj) {
+    usethis::use_r(paste0("objective", i), open = FALSE)
+  }
+  # man/
+  if (!dir.exists(file.path(path, "man"))) {
+    dir.create(file.path(path, "man"))
+  }
+  if ("hello.Rd" %in% list.files(file.path(path, "man"))) {
+    unlink(file.path(path, "man/hello.Rd"))
+  }
+  # inst/
+  dir.create(file.path(path, "inst"))
+  dir.create(file.path(path, "inst/cohorts"))
+  dir.create(file.path(path, "inst/concept_sets"))
+  # extras/
+  dir.create(file.path(path, "extras"))
+  invisible(file.create(file.path(path, "extras/CodeToRun.R")))
+  invisible(file.create(file.path(path, "extras/pullCohortsFromAtlas.R")))
+}
+
+
+#' Insert default test files
+#'
+#' Creates the `tests` folder and populates the `tests/testthat` folder with
+#' a default test file for each script found in the `R` folder.
+#'
+#' @param path Character string identifying the path to the study project,
+#' default `"."`.
+#'
+#' @return
+#' No return value.
+insertTests <- function(
+    path = "."
+    ) {
+
+  usethis::use_testthat()
+
+  if (!dir.exists(file.path(path, "R")) | length(list.files(file.path(path, "R"))) == 0) {
+    cli::cli_abort(
+      message = c(
+        "!" = "No .R files are found to generate tests",
+        "x" = "The R folder in current project doesn't exist or is empty."
+      )
+    )
+  }
+
+  # Create test files for each script in R/ except globals.R
+  for (script in list.files(file.path(path, "R"))) {
+    if (script == "globals.R") {
+      next
+    } else{                                 # remove ".R"
+      usethis::use_test(substr(script, 1, nchar(script) -2), open = FALSE)
+    }
+  }
+}
+
+
+#' Set up study structure
+#'
+#' Creates the standard structure required for a new OMOP study package.
+#' It includes standard folders, R scripts, test and documentation files and it
+#' installs a default list of DARWIN EU®/OHDSI packages.
+#'
+#' It assumes an active R project has already been created and the `renv`
+#' initialized.
+#'
+#' @param path Character string identifying the path to the study project,
+#' default `"."`.
+#' @param n_obj Number of study objectives, default `n_obj = 3`.
+#'
+#' @return
+#' No return value.
+#'
+#' @export
+insertStructure <- function(
+    path = ".",
+    n_obj = 3
+  ) {
+
+  # Need an existing package to run the function
+  if (!file.exists(file.path(path, "DESCRIPTION"))) {
+    cli::cli_abort(
+      message = c(
+        "!" = "The path doesn't correspond to a package folder.",
+        "x" = "A package must contain a DESCRIPTION file. No DESCRIPTION detected at {.path {path}}.",
+        "i" = "Create a package first with {.fn usethis::create_package} or through the RStudio interface."
+      )
+    )
+  }
+
+  # Set up structure at specified project path
+  cli::cli_h1("Setting up study package structure")
+
+  cli::cli_alert_info("Installing package bundle...")
+  installPackageBundle(path)
+
+  cli::cli_alert_info("Inserting documentation files...")
+  insertDocs(path)
+
+  cli::cli_alert_info("Inserting study files...")
+  insertStudyFiles(path, n_obj)
+
+  cli::cli_alert_info("Inserting test files...")
+  insertTests(path)
+
+  cli::cli_alert_success("Package structure created successfully.")
+}

docs/404.md

@@ -0,0 +1,3 @@
+Content not found. Please use links in the navbar.
+
+# Page not found (404)