Merge pull request #104 from FAIRDataPipeline/update-tests

update tests
FAIRDataPipeline · Jul 6, 2021 · 2e00cbc · 2e00cbc
2 parents 1a7ee58 + 77fc02e
commit 2e00cbc
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diff --git a/.github/workflows/test-build.yaml b/.github/workflows/test-build.yaml
@@ -21,10 +21,10 @@ jobs:
       # Define operating systems
       matrix:
         config:
-          - {os: windows-latest, r: 'release'}
+          # - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-16.04, r: '3.6.3'} # Boydorr Server
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          # - {os: ubuntu-16.04, r: '3.6.3'} # Boydorr Server
+          # - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     steps:
       # Checkout repo
@@ -55,6 +55,12 @@ jobs:
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
+      # Install local registry
+      - name: Install registry
+        run: |
+             /bin/bash -c "$(curl -fsSL https://data.scrc.uk/static/localregistry.sh)"
+        shell: bash
+
       # Install system_requirements requirements on macOS
       - name: Install system requirements (macOS-latest)
         if: runner.os == 'macOS'
@@ -64,16 +70,6 @@ jobs:
               brew install gdal
         shell: bash
 
-      # Install system_requirements on ubuntu 16.04 (Boydorr)
-      - name: Install system requirements (ubuntu-16.04)
-        if: matrix.config.os == 'ubuntu-16.04'
-        run : |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "16.04"), sep = "\n")')
-        shell: bash
-
       # Install system requirements on ubuntu 20.04
       - name: Install system requirements (ubuntu-20.04)
         if: matrix.config.os == 'ubuntu-20.04'
@@ -91,120 +87,18 @@ jobs:
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
-      # Run CMD check on all but Boydorr (convert2grid test will fail on Boydorr)
-      # Use SCRC_API_TOKEN (PAT from Jonathan Hollocombe) to interact with the data
-      # registry
-      - name: Check (All but Boydorr)
-        if: matrix.config.os != 'ubuntu-16.04'
+      # Run CMD check
+      - name: Run CMD check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
-          SCRC_API_TOKEN: ${{ secrets.SCRC_API_TOKEN }}
           R_CHECK_SYSTEM_CLOCK: 0
         run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
-      # Run CMD check on Boydorr usinging BOYDORR: "TRUE" to skip convert2grid test
-      # Use SCRC_API_TOKEN (PAT from Jonathan Hollocombe) to interact with the data
-      # registry
-      - name: Check (Boydorr)
-        if: matrix.config.os == 'ubuntu-16.04'
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-          SCRC_API_TOKEN: ${{ secrets.SCRC_API_TOKEN }}
-          BOYDORR: "TRUE"
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
       # If anything fails upload results to artifacts
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@main
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
-
-# Coverage ------------------------------------------------------------------
-# Located within the macOS-latest (release) job
-
-      - name: Test coverage (setup)
-        # Only when main is pushed
-        if: github.event_name == 'push' && github.ref == 'refs/heads/main' && runner.os == 'macOS'
-        # Use the default GITHUB_TOKEN as an enviromental version for all steps
-        env:
-          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-        # Setup keychain needed to cache github token for upload_toml_to_github test
-        uses: sinoru/[email protected]
-
-      # Add github Personal Access Token to keychain:
-      # * Needed for upload_toml_to_github test
-      # * Echoes to git credential-osxkeychain
-      # * This emulate stdin() line by line
-      - name: Add credentials in keychain
-        if: github.event_name == 'push' && github.ref == 'refs/heads/main' && runner.os == 'macOS'
-        env:
-          GITHUB_TOKEN: ${{ secrets.SCRC_API_PAT }}
-        run: |
-          echo "\
-          protocol=https
-          host=github.com
-          username=Personal Access Token
-          password=$GITHUB_TOKEN" | git credential-osxkeychain store
-
-      # Run code coverage with RUN_TEST to enable upload_toml_to_github test
-      # Use SCRC_API_TOKEN (PAT from Jonathan Hollocombe) to interact with the data
-      # registry
-      - name: Test coverage
-        if: github.event_name == 'push' && github.ref == 'refs/heads/main' && runner.os == 'macOS'
-        env:
-          SCRC_API_TOKEN: ${{ secrets.SCRC_API_TOKEN }}
-          RUN_TEST: "TRUE"
-        run: |
-          remotes::install_cran("covr")
-          covr::codecov()
-        shell: Rscript {0}
-
-# Build and deploy DOCS -----------------------------------------------------
-# Located within the macOS-latest (release) job
-
-      - name: Build and deploy docs (setup)
-        # Only when main is pushed
-        if: github.event_name == 'push' && github.ref == 'refs/heads/main' && runner.os == 'macOS'
-        # Setup pandoc needed to build docs
-        uses: r-lib/actions/setup-pandoc@v1
-
-      # Install Mac OS requirements
-      - name: Build and deploy docs (system requirements)
-        if: github.event_name == 'push' && github.ref == 'refs/heads/main' && runner.os == 'macOS'
-        run : |
-              brew install harfbuzz
-              brew install fribidi
-        shell: bash
-
-      # Build documentation with pkgdown
-      - name: Build Docs
-        if: github.event_name == 'push' && github.ref == 'refs/heads/mains' && runner.os == 'macOS'
-        run: |
-          install.packages("pkgdown")
-          pkgdown::build_site()
-        shell: Rscript {0}
-
-      # Create a development branch and commit to it
-      - name: Commit to development branch
-        if: github.event_name == 'push' && github.ref == 'refs/heads/main' && runner.os == 'macOS'
-        run: |
-          git checkout -b development
-          git add .
-          git commit -m '[skip ci]'
-        shell: bash
-
-      # Deploy the docs using JamesIves/github-pages-deploy-action
-      - name: Deploy Docs
-        if: github.event_name == 'push' && github.ref == 'refs/heads/main' && runner.os == 'macOS'
-        uses: JamesIves/github-pages-deploy-action@releases/v3
-        with:
-          GITHUB_TOKEN: ${{ secrets.SCRC_API_PAT }}
-          BASE_BRANCH: development
-          BRANCH: main # The branch the action should deploy to.
-          FOLDER: docs # The folder the action should deploy.
-          TARGET_FOLDER: docs
-          COMMIT_MESSAGE: 'build docs [skip ci]'
diff --git a/R/fair_pull.R b/R/fair_pull.R
@@ -1,10 +1,12 @@
 #' fair_pull
 #'
 #' @param path path
+#' @param endpoint a \code{string} specifying the registry endpoint
 #'
 #' @export
 #'
-fair_pull <- function(path = "config.yaml") {
+fair_pull <- function(path = "config.yaml",
+                      endpoint = "http://localhost:8000/api/") {
 
   run_server()
 
@@ -47,7 +49,8 @@ fair_pull <- function(path = "config.yaml") {
     # Download raw data to data store and register in data registry
     for (i in seq_along(register)) {
       register_external_object(yaml = yaml,
-                               register_this = register[[i]])
+                               register_this = register[[i]],
+                               endpoint = endpoint)
     }
   }
 

diff --git a/R/fair_run.R b/R/fair_run.R
@@ -2,10 +2,13 @@
 #'
 #' @param path string
 #' @param skip don't bother checking whether the repo is clean
+#' @param endpoint a \code{string} specifying the registry endpoint
 #'
 #' @export
 #'
-fair_run <- function(path = "config.yaml", skip = FALSE) {
+fair_run <- function(path = "config.yaml",
+                     endpoint = "http://localhost:8000/api/",
+                     skip = FALSE) {
 
   run_server()
 
@@ -156,7 +159,8 @@ fair_run <- function(path = "config.yaml", skip = FALSE) {
 
         entries <- get_entry("data_product",
                              list(name = write_dataproduct,
-                                  namespace = write_namespace_id))
+                                  namespace = write_namespace_id),
+                             endpoint = endpoint)
 
         if (is.null(entries)) {
           write_version <- "0.0.1"

diff --git a/R/get_entry.R b/R/get_entry.R
@@ -22,8 +22,10 @@ get_entry <- function(table, query, endpoint = "http://localhost:8000/api/") {
 
   is_queryable(table, query)
 
-  output <- httr::GET(paste0(endpoint, table, ""),
-                      query = query,
+  api_url <- paste0(endpoint, table)
+  api_url <- file.path(dirname(api_url), basename(api_url), "")
+
+  output <- httr::GET(api_url, query = query,
                       httr::add_headers(.headers = h)) %>%
     httr::content(as = "text", encoding = "UTF-8") %>%
     jsonlite::fromJSON(simplifyVector = FALSE)

diff --git a/R/get_existing.R b/R/get_existing.R
@@ -7,6 +7,7 @@
 #' the results, default is \code{TRUE}
 #' @param detail a \code{string} specifying what level of detail to return;
 #' options are \code{"all"} for all details or \code{"id"} for just URL and IDs
+#' @param endpoint a \code{string} specifying the registry endpoint
 #'
 #' @return Returns a \code{data.frame} of entries in table, default is limited
 #' to 100 entries
@@ -24,7 +25,10 @@
 #' get_existing("data_product")
 #' }
 #'
-get_existing <- function(table, limit_results = TRUE, detail = "all") {
+get_existing <- function(table,
+                         limit_results = TRUE,
+                         detail = "all",
+                         endpoint = "http://localhost:8000/api/") {
 
   if (!check_table_exists(table))
     usethis::ui_stop(paste(
@@ -34,11 +38,13 @@ get_existing <- function(table, limit_results = TRUE, detail = "all") {
   key <- get_token()
   h <- c(Authorization = paste("token", key))
 
+  api_url <- paste0(endpoint, table)
+  api_url <- file.path(dirname(api_url), basename(api_url), "")
+
   tryCatch({
 
     # Get the 100 newest results
-    output <- httr::GET(paste("http://localhost:8000/api", table, "",
-                              sep = "/"),
+    output <- httr::GET(api_url,
                         httr::add_headers(.headers = h)) %>%
       httr::content(as = "text", encoding = "UTF-8") %>%
       jsonlite::fromJSON(simplifyVector = FALSE)

diff --git a/R/get_fields.R b/R/get_fields.R
@@ -3,13 +3,15 @@
 #' Use API endpoint to produce a list of fields for a table. Requires API key.
 #'
 #' @param table a \code{string} specifying the name of the table
+#' @param endpoint a \code{string} specifying the registry endpoint
 #'
 #' @return Returns a \code{data.frame} of fields and their attributes set to
 #' "none"
+#'
 #' @export
 #' @keywords internal
 #'
-get_fields <- function(table){
+get_fields <- function(table, endpoint = "http://localhost:8000/api/"){
 
   # Users and Groups are valid tables but cannot be posted to
   if (table == "users" | table == "groups")
@@ -19,9 +21,11 @@ get_fields <- function(table){
   key <- get_token()
   h <- c(Authorization = paste("token", key))
 
+  api_url <- paste0(endpoint, table)
+  api_url <- file.path(dirname(api_url), basename(api_url), "")
+
   # Perform an options request
-  out <- httr::VERB("OPTIONS", paste("http://localhost:8000/api", table, "",
-                                     sep = "/"),
+  out <- httr::VERB("OPTIONS", api_url,
                     httr::add_headers(.headers = h)) %>%
     httr::content(as = "text", encoding = "UTF-8") %>%
     jsonlite::fromJSON(simplifyVector = FALSE)

diff --git a/R/get_table_optional.R b/R/get_table_optional.R
@@ -1,15 +1,16 @@
 #' Get optional fields
 #'
 #' @param table a \code{string} specifying the name of the table
+#' @param endpoint a \code{string} specifying the registry endpoint
 #'
-#' @return Returns a \code{data.frame} of optional fields and thier properties
+#' @return Returns a \code{data.frame} of optional fields and their properties
 #' @export
 #' @keywords internal
 #'
-get_table_optional <- function(table){
+get_table_optional <- function(table, endpoint){
   # if(! check_table_exists(table))
   #   stop("Unknown Table")
-  optional <- get_fields(table) %>%
+  optional <- get_fields(table, endpoint) %>%
     filter(!.data$read_only) %>%
     filter(!.data$required)
 }
diff --git a/R/get_table_queryable.R b/R/get_table_queryable.R
@@ -1,14 +1,18 @@
 #' Get queryable fields
 #'
 #' @param table a \code{string} specifying the name of the table
+#' @param endpoint a \code{string} specifying the registry endpoint
 #'
 #' @return Returns a character vector of queryable fields
 #' @export
 #' @keywords internal
 #'
-get_table_queryable <- function(table) {
-  out <- httr::VERB("OPTIONS", paste("http://localhost:8000/api", table, "",
-                                     sep = "/")) %>%
+get_table_queryable <- function(table, endpoint) {
+
+  api_url <- paste0(endpoint, table)
+  api_url <- file.path(dirname(api_url), basename(api_url), "")
+
+  out <- httr::VERB("OPTIONS", api_url) %>%
     httr::content(as = "text", encoding = "UTF-8") %>%
     jsonlite::fromJSON(simplifyVector = FALSE)
   as.character(out$filter_fields)

diff --git a/R/get_table_readable.R b/R/get_table_readable.R
@@ -1,13 +1,14 @@
 #' Get readable fields
 #'
 #' @param table name of table
+#' @param endpoint a \code{string} specifying the registry endpoint
 #'
 #' @return a dataframe of readable fields and their properties
 #' @export
 #' @keywords internal
 #'
-get_table_readable <- function(table){
+get_table_readable <- function(table, endpoint){
   # if(! check_table_exists(table))
   #   stop("Unknown Table")
-  readable <- get_fields(table)
+  readable <- get_fields(table, endpoint)
 }
diff --git a/R/get_table_writable.R b/R/get_table_writable.R
@@ -1,15 +1,16 @@
 #' Get writable fields
 #'
 #' @param table a \code{string} specifying the name of the table
+#' @param endpoint a \code{string} specifying the registry endpoint
 #'
 #' @return Returns a character vector of writable fields
 #' @export
 #' @keywords internal
 #'
-get_table_writable <- function(table){
+get_table_writable <- function(table, endpoint){
   # if(!check_table_exists(table))
   #   stop("Unknown Table")
 
-  get_fields(table) %>%
+  get_fields(table, endpoint) %>%
     filter(!.data$read_only)
 }
diff --git a/R/get_tables.R b/R/get_tables.R
@@ -1,14 +1,15 @@
 #' Get tables from registry
 #'
 #' Use api endpoint to produce a list of tables
-#' @param live whether or not to get the tables directly from the API
+#' @param endpoint a \code{string} specifying the registry endpoint
 #'
 #' @return a character vector of tables
 #' @export
 #' @keywords internal
 #'
-get_tables <- function(live = FALSE){
-  httr::GET(paste("http://localhost:8000/api", "", sep = "/")) %>%
+get_tables <- function(endpoint = "http://localhost:8000/api/"){
+
+  httr::GET(endpoint) %>%
     httr::content(as = "text", encoding = "UTF-8") %>%
     jsonlite::fromJSON(simplifyVector = FALSE) %>%
     names()