Integrate CLI with unit tests

.github/workflows/pkgdown.yaml

@@ -16,9 +16,9 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |

.github/workflows/test-build.yaml

@@ -24,13 +24,13 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-pandoc@master
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
             rcmdcheck

.github/workflows/test-coverage.yaml

@@ -9,25 +9,31 @@ name: test-coverage
 
 jobs:
   test-coverage:
+     # If the commit message isn't [skip ci]
+    if: "!contains(github.event.commits[0].message, '[skip ci]')"
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: covr
+          extra-packages: |
+            covr
+            remotes
 
       - name: Install local registry
         run: /bin/bash -c "$(curl -fsSL https://data.scrc.uk/static/localregistry.sh)"
       - name: Start registry
         run: $HOME/.fair/registry/scripts/start_fair_registry
 
+      - name: Install R API
+        run: Rscript -e 'remotes::install_local(upgrade = "never")'
+
       - name: init
         run: |
           rDataPipeline::fair_init(

.gitignore

@@ -49,4 +49,5 @@ docs
 /config_files
 /test
 /tests/testthat/test
-sonia.yaml
+/data_store
+sandbox.R

DESCRIPTION

@@ -11,7 +11,6 @@ Description: R implementation of the 'FAIR Data Pipeline API'. The 'FAIR Data
 License: GPL (>= 3)
 Imports:
     assertthat,
-    cli,
     configr,
     dplyr,
     git2r,
@@ -27,7 +26,9 @@ Imports:
     yaml
 Suggests:
     units,
-    testthat
+    here,
+    testthat,
+    reticulate
 biocViews: 
     rhdf5
 Encoding: UTF-8

NAMESPACE

@@ -12,7 +12,6 @@ export(find_write_match)
 export(findme)
 export(get_components)
 export(get_dataproduct)
-export(get_entry)
 export(initialise)
 export(link_read)
 export(link_write)
@@ -31,7 +30,6 @@ export(write_estimate)
 export(write_table)
 import(R6)
 import(assertthat, except = has_name)
-import(cli)
 import(configr)
 import(dplyr)
 import(httr)

R/add_read.R

@@ -3,33 +3,17 @@
 #' Add data product to `read` block of user-written config file. Used in
 #' combination with \code{create_config()} for unit testing.
 #'
-#' @param path config file path
-#' @param data_product data_product field
-#' @param component component field
-#' @param version (optional) version field
-#' @param use_data_product (optional) use_data_product field
-#' @param use_component (optional) use_component field
-#' @param use_version (optional) use_version field
-#' @param use_namespace (optional) use_namespace field
+#' @param path user-written config.yaml file path
+#' @param data_product `data_product:` field
+#' @param component `component:` field
+#' @param version (optional) `version:` field
+#' @param use_data_product (optional) `use: data_product:` field
+#' @param use_component (optional) `use: component:` field
+#' @param use_version (optional) `use: version:` field
+#' @param use_namespace (optional) `use: namespace:` field
 #'
 #' @export
-#'
-#' @examples
-#' \dontrun{
-#' path <- "test_config/config.yaml"
-#'
-#' # Write run_metadata block
-#' create_config(path = path,
-#'               description = "test",
-#'               input_namespace = "test_user",
-#'               output_namespace = "test_user")
-#'
-#' # Write read block
-#' add_read(path = path,
-#'          data_product = "test/array",
-#'          component = "level/a/s/d/f/s",
-#'          version = "0.2.0")
-#' }
+#' @keywords internal
 #'
 add_read <- function(path,
                      data_product,
@@ -76,4 +60,5 @@ add_read <- function(path,
                      file = path)
   }
 
+  invisible(path)
 }

R/add_write.R

@@ -3,34 +3,19 @@
 #' Add data product to `read` block of user-written config file. Used in
 #' combination with \code{create_config()} for unit testing.
 #'
-#' @param path config file path
-#' @param data_product data_product field
-#' @param description component field
-#' @param version (optional) version field
-#' @param file_type (optional) file type field
-#' @param use_data_product (optional) use_data_product field
-#' @param use_component (optional) use_component field
-#' @param use_version (optional) use_version field
-#' @param use_namespace (optional) use_namespace field
+#' @param path user-written config.yaml file path
+#' @param data_product `data_product:` field
+#' @param description `component:` field
+#' @param version (optional) `version:` field
+#' @param file_type (optional) `file_type:` field
+#' @param use_data_product (optional) `use: data_product:` field
+#' @param use_component (optional) `use: component:` field
+#' @param use_version (optional) `use: version:` field
+#' @param use_namespace (optional) `use: namespace:` field
+#' @param use_public (optional) `use: public:` field
 #'
 #' @export
-#'
-#' @examples
-#' \dontrun{
-#' path <- "test_config/config.yaml"
-#'
-#' # Write run_metadata block
-#' create_config(path = path,
-#'               description = "test",
-#'               input_namespace = "test_user",
-#'               output_namespace = "test_user")
-#'
-#' # Write read block
-#' add_write(path = path,
-#'           data_product = "test/array",
-#'           description = "data product description",
-#'           version = "0.2.0")
-#' }
+#' @keywords internal
 #'
 add_write <- function(path,
                       data_product,
@@ -40,7 +25,8 @@ add_write <- function(path,
                       use_data_product,
                       use_component,
                       use_version,
-                      use_namespace) {
+                      use_namespace,
+                      use_public) {
 
   # Generate write block
   new_write <- list()
@@ -53,6 +39,7 @@ add_write <- function(path,
   if (!missing(use_component)) new_write$use$component <- use_component
   if (!missing(use_version)) new_write$use$version <- use_version
   if (!missing(use_namespace)) new_write$use$namespace <- use_namespace
+  if (!missing(use_public)) new_write$use$public <- use_public
 
   # Read file contents
   contents <- configr::read.config(file = path)
@@ -79,4 +66,5 @@ add_write <- function(path,
                      file = path)
   }
 
+  invisible(path)
 }

R/check_config.R

@@ -5,6 +5,8 @@
 #' @param data_product data_product
 #' @param what what
 #'
+#' @noRd
+#'
 check_config <- function(handle, data_product, what) {
 
   error <- paste(usethis::ui_field(data_product), "missing from config file")

R/check_dataproduct_exists.R

@@ -8,6 +8,8 @@
 #' @param write_namespace_id write_namespace_id
 #' @param endpoint endpoint
 #'
+#' @noRd
+#'
 check_dataproduct_exists <- function(write_dataproduct,
                                      write_version,
                                      write_namespace_id,

R/check_datetime.R

@@ -5,6 +5,8 @@
 #' @param query_class a \code{string} specifying the class of the field
 #' @param this_query a \code{string} specifying the contents of the field
 #'
+#' @noRd
+#'
 check_datetime <- function(table,
                            this_field,
                            query_class,

R/check_exists.R

@@ -8,6 +8,7 @@
 #'
 #' @return Returns \code{TRUE} if the entry exists and \code{FALSE} if it
 #' doesn't
+#' @noRd
 #'
 check_exists <- function(table,
                          query) {

R/check_field.R

@@ -7,6 +7,8 @@
 #' @param method a \code{string} specifying the method, c("GET", "POST")
 #' @param endpoint endpoint
 #'
+#' @noRd
+#'
 check_field <- function(table,
                         this_field,
                         query_class,

R/check_fields.R

@@ -5,6 +5,8 @@
 #' @param method a \code{string} specifying the method, c("GET", "POST")
 #' @param endpoint endpoint
 #'
+#' @noRd
+#'
 check_fields <- function(table, query, method, endpoint) {
 
   fields <- names(query)

R/check_handle.R

@@ -6,6 +6,8 @@
 #' @param what element in handle -- one of c("inputs", "outputs")
 #' @param component a \code{string} specifying the name of the component
 #'
+#' @noRd
+#'
 check_handle <- function(handle, data_product, what, component) {
 
   # link_read() / link_write() functions

R/check_integer.R

@@ -5,6 +5,8 @@
 #' @param query_class a \code{string} specifying the class of the field
 #' @param this_query a \code{string} specifying the contents of the field
 #'
+#' @noRd
+#'
 check_integer <- function(table,
                           this_field,
                           query_class,

R/check_local_repo.R

@@ -1,7 +1,9 @@
 #' check_local_repo
 #'
 #' @param path Local repository file path
+#'
 #' @return \code{boolean}, if local repository is clean (TRUE, else FALSE)
+#' @noRd
 #'
 check_local_repo <- function(path) {
   if (grepl("^~", path)) path <- gsub("^~", "", path)

R/check_string.R

@@ -4,6 +4,8 @@
 #' @param this_field a \code{string} specifying the name of the field
 #' @param this_query a \code{string} specifying the contents of the field
 #'
+#' @noRd
+#'
 check_string <- function(table,
                          this_field,
                          this_query) {

R/check_table_exists.R

@@ -5,6 +5,7 @@
 #' @param table a \code{string} specifying the name of the table
 #'
 #' @return Returns \code{TRUE} if a table exists, \code{FALSE} if it doesn't
+#' @noRd
 #'
 check_table_exists <- function(table) {
   if (!is.character(table))

R/check_yaml_write.R

@@ -3,6 +3,8 @@
 #' @param handle \code{fdp} object
 #' @param data_product a \code{string} specifying the name of the data product
 #'
+#' @noRd
+#'
 check_yaml_write <- function(handle, data_product) {
 
   endpoint <- handle$yaml$run_metadata$local_data_registry_url

R/class-fdp.R

@@ -4,6 +4,7 @@
 #'
 #' @name fdp-class
 #' @rdname fdp-class
+#' @keywords internal
 #'
 fdp <- R6::R6Class("fdp", list(
   #' @field yaml a \code{list} containing the contents of the working
@@ -85,32 +86,31 @@ fdp <- R6::R6Class("fdp", list(
   #'
   print = function(...) {
 
-    contains_yaml <- !is.null(self$yaml)
-    contains_dir <- !is.null(self$fdp_config_dir)
-    contains_config <- !is.null(self$model_config)
-    contains_script <- !is.null(self$submission_script)
-    contains_coderun <- !is.null(self$code_run)
-
-    cat("Contains:\n")
-    if (contains_yaml) cat("- Config file\n")
-    if (contains_dir) cat("- Config dir\n")
-    if (contains_config) cat("- Config file URL\n")
-    if (contains_script) cat("- Submission script URL\n")
-    if (contains_coderun) cat("- Code run URL\n")
-
-    if (!is.null(self$inputs)) {
-      cat("\n\n", "Inputs:", "\n")
+    if (!is.null(self$yaml)) {
+      msg <- "Code run: {ui_value(self$yaml$run_metadata$description)}"
+      usethis::ui_info(msg)
+    }
+
+    if (is.null(self$inputs)) {
+      msg <- "None"
+      usethis::ui_info("Inputs: {ui_value(msg)}")
+
+    } else {
+      usethis::ui_info("Inputs:")
       self$inputs %>%
         dplyr::select(data_product) %>%
         print()
     }
 
-    if (!is.null(self$outputs)) {
-      cat("\n\n", "outputs:", "\n")
-      tmp <- self$outputs %>%
-        dplyr::select(use_component, use_data_product, use_version)
-      names(tmp) <- gsub("use_", "", names(tmp))
-      print(tmp)
+    if (is.null(self$outputs)) {
+      msg <- "None"
+      usethis::ui_info("Outputs: {ui_value(msg)}")
+
+    } else {
+      usethis::ui_info("Outputs:")
+      self$outputs %>%
+        dplyr::select(use_data_product, use_component, use_version) %>%
+        print()
     }
 
     invisible(self)