Merge pull request #205 from FAIRDataPipeline/fix-new-r

Fix new r

.github/workflows/pkgdown.yaml

@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
 
@@ -32,7 +32,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Restore R package cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

.github/workflows/test-build.yaml

@@ -3,9 +3,6 @@ on:
     branches:
       - '*'
   workflow_dispatch:
-#  pull_request:
-#    branches:
-#      - master
 
 jobs:
   R-CMD-check:
@@ -17,14 +14,14 @@ jobs:
       fail-fast: false
       matrix:
         config:
-#          - {os: windows-latest, r: 'release'}
-#          - {os: macOS-latest, r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
           - {os: ubuntu-latest, r: 'release'}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: r-lib/actions/setup-pandoc@v2
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -37,14 +34,11 @@ jobs:
             rcmdcheck
             remotes
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
-          architecture: 'x64'
-      - name: Install local registry
-        run: curl -fsSL https://data.scrc.uk/static/localregistry.sh | /bin/bash -s -- -b main
+          python-version: '3.12'
       - name: Checkout FAIRDataPipeline/FAIR-CLI
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: FAIRDataPipeline/FAIR-CLI
           path: FAIR-CLI
@@ -60,25 +54,25 @@ jobs:
         run: |
           cd ../FAIR-CLI
           poetry install
-          source .venv/bin/activate
-          cd ${{ github.workspace }}
+          source $VENV
+          cd '${{ github.workspace }}'
+          fair registry install --version main
           fair init --ci
           fair registry start
+        shell: bash
+
+      - name: Copy token on windows
+        run: |
+          mkdir -p C:/Users/runneradmin/Documents/.fair/registry/
+          cp C:/Users/runneradmin/.fair/registry/token C:/Users/runneradmin/Documents/.fair/registry/token
+        shell: bash
+        if: runner.os == 'Windows'
 
       - name: Install R API system requirements (macOS-latest)
         if: runner.os == 'macOS'
         run : |
-              rm '/usr/local/bin/gfortran'
               brew install hdf5
               brew install gdal
-      - name: Install R API system requirements (ubuntu-20.04)
-        if: matrix.config.os == 'ubuntu-20.04'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
-
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_: false
@@ -88,12 +82,14 @@ jobs:
           rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
       - name: Show testthat output
-        if: always()
+        if: ${{ !cancelled() }}
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
       - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
+          overwrite: true
+          include-hidden-files: true

.github/workflows/test-coverage.yaml

@@ -59,7 +59,7 @@ jobs:
           rDataPipeline::fair_init(
             name = "Sonia Mitchell",
             identifier = "https://orcid.org/0000-0003-1536-2066",
-            endpoint = "http://localhost:8000/api/")
+            endpoint = "http://127.0.0.1:8000/api/")
         shell: Rscript {0}
       - name: Test coverage
         env:

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rDataPipeline
 Title: Functions to Interact with the 'FAIR Data Pipeline'
-Version: 0.6.0
-Authors@R: c(person("Sonia", "Mitchell", email = "[email protected]",
+Version: 0.60.0
+Authors@R: c(person("Sonia", "Mitchell",
                   role = c("aut"), comment = c(ORCID = "0000-0003-1536-2066")),
              person("Ryan", "Field", email = "[email protected]", role = c("cre", "aut"), 
                   comment = c(ORCID = "0000-0002-4424-9890")))

NEWS.md

@@ -1,7 +1,7 @@
 # NEWS
-# rDataPipeline v0.6.0
+# rDataPipeline v0.60.0
 ## Improvements:
-  Updates to work with latest versions of R
+  Updates to work with latest version of data registry
 - v0.54.1
   - Initial release
 - v0.54.2

R/check_dataproduct_exists.R

@@ -21,7 +21,7 @@ check_dataproduct_exists <- function(write_dataproduct,
                                  namespace = write_namespace_id),
                             endpoint = endpoint)
 
-  write_namespace_url <- file.path("http://localhost:8000", "api",
+  write_namespace_url <- file.path("http://127.0.0.1:8000", "api",
                                    "namespace", write_namespace_id)
   write_namespace <- get_entity(write_namespace_url)$name
 

R/check_exists.R

@@ -14,7 +14,7 @@
 check_exists <- function(table,
                          query) {
 
-  output <- httr::GET(paste0("http://localhost:8000/api/", table, ""),
+  output <- httr::GET(paste0("http://127.0.0.1:8000/api/", table, ""),
                       query = query)
 
   if (any(names(output) == "status_code")) {

R/create_config.R

@@ -33,7 +33,7 @@ create_config <- function(path,
 
   # Generate run_metadata block
   run_metadata <- list(description = description,
-                       local_data_registry_url = "http://localhost:8000/api/",
+                       local_data_registry_url = "http://127.0.0.1:8000/api/",
                        remote_data_registry_url = "https://data.scrc.uk/api/",
                        default_input_namespace = input_namespace,
                        default_output_namespace = output_namespace,

R/fair_init.R

@@ -11,7 +11,7 @@
 #'
 fair_init <- function(name,
                       identifier,
-                      endpoint = "http://localhost:8000/api/") {
+                      endpoint = "http://127.0.0.1:8000/api/") {
 
   user_url <- get_url(table = "users",
                       query = list(username = "admin"),

R/fair_run.R

@@ -7,7 +7,7 @@
 #' @export
 #'
 fair_run <- function(path = "config.yaml",
-                     endpoint = "http://localhost:8000/api/",
+                     endpoint = "http://127.0.0.1:8000/api/",
                      skip = FALSE) {
 
   # Save names in data store

R/get_dataproduct.R

@@ -10,7 +10,7 @@
 get_dataproduct <- function(data_product,
                             version,
                             namespace,
-                            endpoint = "http://localhost:8000/api/") {
+                            endpoint = "http://127.0.0.1:8000/api/") {
   # Get provenance URL
   namespace_entry <- get_entry("namespace",
                                list(name = namespace),

R/get_entity.R

@@ -11,7 +11,7 @@ get_entity <- function(url) {
 
   # Sometimes an error is returned from the local registry:
   #   "Error in curl::curl_fetch_memory(url, handle = handle) :
-  #    Failed to connect to localhost port 8000: Connection refused"
+  #    Failed to connect to 127.0.0.1:8000 port 8000: Connection refused"
   # Repeating the action works eventually...
   continue <- TRUE
   while (continue) {

R/get_entry.R

@@ -10,7 +10,7 @@
 #' @export
 #' @family get functions
 #'
-get_entry <- function(table, query, endpoint = "http://localhost:8000/api/") {
+get_entry <- function(table, query, endpoint = "http://127.0.0.1:8000/api/") {
 
   key <- get_token()
   h <- c(Authorization = paste("token", key))

R/get_existing.R

@@ -19,7 +19,7 @@
 get_existing <- function(table,
                          limit_results = TRUE,
                          detail = "all",
-                         endpoint = "http://localhost:8000/api/") {
+                         endpoint = "http://127.0.0.1:8000/api/") {
 
   if (!check_table_exists(table))
     usethis::ui_stop(paste(

R/get_fields.R

@@ -10,7 +10,7 @@
 #' @return Returns a \code{data.frame} of fields and their attributes set to
 #' "none"
 #'
-get_fields <- function(table, endpoint = "http://localhost:8000/api/") {
+get_fields <- function(table, endpoint = "http://127.0.0.1:8000/api/") {
 
   # Add token to options request header
   key <- get_token()

R/get_id.R

@@ -14,7 +14,7 @@
 #'
 get_id <- function(table,
                    query = list(),
-                   endpoint = "http://localhost:8000/api/") {
+                   endpoint = "http://127.0.0.1:8000/api/") {
 
   output <- get_entry(table, query, endpoint)
 

R/get_tables.R

@@ -6,7 +6,7 @@
 #' @return a character vector of tables
 #' @keywords internal
 #'
-get_tables <- function(endpoint = "http://localhost:8000/api/") {
+get_tables <- function(endpoint = "http://127.0.0.1:8000/api/") {
 
   httr::GET(endpoint) %>%
     httr::content(as = "text", encoding = "UTF-8") %>%

R/get_url.R

@@ -14,7 +14,7 @@
 #'
 get_url <- function(table,
                     query = list(),
-                    endpoint = "http://localhost:8000/api/") {
+                    endpoint = "http://127.0.0.1:8000/api/") {
 
   output <- get_entry(table = table,
                       query = query,

R/new_author.R

@@ -15,7 +15,7 @@
 #'
 new_author <- function(name,
                        identifier,
-                       endpoint = "http://localhost:8000/api/") {
+                       endpoint = "http://127.0.0.1:8000/api/") {
 
   data <- list()
 

R/new_code_repo_release.R

@@ -19,7 +19,7 @@ new_code_repo_release <- function(name,
                                   version,
                                   object_url,
                                   website,
-                                  endpoint = "http://localhost:8000/api/") {
+                                  endpoint = "http://127.0.0.1:8000/api/") {
 
   data <- list(name = name,
                version = version,

R/new_code_run.R

@@ -31,7 +31,7 @@ new_code_run <- function(run_date,
                          submission_script_url,
                          inputs_urls = list(),
                          outputs_urls = list(),
-                         endpoint = "http://localhost:8000/api/") {
+                         endpoint = "http://127.0.0.1:8000/api/") {
 
   data <- list(run_date = run_date,
                inputs = inputs_urls,

R/new_data_product.R

@@ -19,7 +19,7 @@ new_data_product <- function(name,
                              version,
                              object_url,
                              namespace_url,
-                             endpoint = "http://localhost:8000/api/") {
+                             endpoint = "http://127.0.0.1:8000/api/") {
 
   post_data(table = "data_product",
             data =  list(name = name,

R/new_external_object.R

@@ -30,7 +30,7 @@ new_external_object <- function(doi_or_unique_name,
                                 description,
                                 data_product_url,
                                 original_store_url,
-                                endpoint = "http://localhost:8000/api/") {
+                                endpoint = "http://127.0.0.1:8000/api/") {
 
   data <- list(doi_or_unique_name = doi_or_unique_name,
                release_date = release_date,

R/new_file_type.R

@@ -12,7 +12,7 @@
 #'
 new_file_type <- function(name,
                           extension,
-                          endpoint = "http://localhost:8000/api/") {
+                          endpoint = "http://127.0.0.1:8000/api/") {
 
   post_data(table = "file_type",
             data =  list(name = name,

R/new_issue.R

@@ -16,7 +16,7 @@
 new_issue <- function(severity,
                       description,
                       component_issues,
-                      endpoint = "http://localhost:8000/api/") {
+                      endpoint = "http://127.0.0.1:8000/api/") {
 
   post_data(table = "issue",
             data =  list(severity = severity,

R/new_keyword.R

@@ -16,7 +16,7 @@
 new_keyword <- function(object_url,
                         keyphrase,
                         identifier,
-                        endpoint = "http://localhost:8000/api/") {
+                        endpoint = "http://127.0.0.1:8000/api/") {
 
   data <- list(object = object_url,
                keyphrase = keyphrase)

R/new_licence.R

@@ -13,7 +13,7 @@
 #'
 new_licence <- function(object_url,
                         licence_info,
-                        endpoint = "http://localhost:8000/api/") {
+                        endpoint = "http://127.0.0.1:8000/api/") {
 
   post_data(table = "licence",
             data =  list(object = object_url,

R/new_namespace.R

@@ -16,7 +16,7 @@
 new_namespace <- function(name,
                           full_name,
                           website,
-                          endpoint = "http://localhost:8000/api/") {
+                          endpoint = "http://127.0.0.1:8000/api/") {
 
   data <- list(name = name)
 

R/new_object.R

@@ -20,7 +20,7 @@ new_object <- function(description,
                        storage_location_url,
                        authors_url,
                        file_type_url,
-                       endpoint = "http://localhost:8000/api/") {
+                       endpoint = "http://127.0.0.1:8000/api/") {
 
   data <- list()
 

R/new_object_component.R

@@ -30,7 +30,7 @@ new_object_component <- function(object_url,
                                  description,
                                  whole_object = FALSE,
                                  issues_urls,
-                                 endpoint = "http://localhost:8000/api/") {
+                                 endpoint = "http://127.0.0.1:8000/api/") {
 
   data <- list(object = object_url,
                name = name,

R/new_quality_controlled.R

@@ -11,7 +11,7 @@
 #' @family new functions
 #'
 new_quality_controlled <- function(object_url,
-                                   endpoint = "http://localhost:8000/api/") {
+                                   endpoint = "http://127.0.0.1:8000/api/") {
 
   post_data(table = "quality_controlled",
             data = list(object = object_url),

R/new_storage_location.R

@@ -21,7 +21,7 @@ new_storage_location <- function(path,
                                  hash,
                                  public,
                                  storage_root_url,
-                                 endpoint = "http://localhost:8000/api/") {
+                                 endpoint = "http://127.0.0.1:8000/api/") {
   data <- list(path = path,
                hash = hash,
                storage_root = storage_root_url)

R/new_storage_root.R

@@ -15,7 +15,7 @@
 #'
 new_storage_root <- function(root,
                              local,
-                             endpoint = "http://localhost:8000/api/") {
+                             endpoint = "http://127.0.0.1:8000/api/") {
 
   data <- list(root = root)