Merge pull request #157 from FAIRDataPipeline/integrate-cli

Integrate cli

.github/workflows/test-build.yaml

@@ -32,27 +32,66 @@ jobs:
           use-public-rspm: true
       - uses: r-lib/actions/setup-r-dependencies@v1
         with:
-          extra-packages: rcmdcheck
+          extra-packages: |
+            rcmdcheck
+            remotes
+
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+      - name: Install local registry
+        run: /bin/bash -c "$(curl -fsSL https://data.scrc.uk/static/localregistry.sh)"
+      - name: Checkout FAIRDataPipeline/FAIR-CLI
+        uses: actions/checkout@v2
+        with:
+          repository: FAIRDataPipeline/FAIR-CLI
+          path: FAIR-CLI
+      - name: Move FAIR-CLI
+        run: mv FAIR-CLI ../FAIR-CLI
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      - name: Install and initialise FAIR CLI
+        if: runner.os == 'macOS'
+        run: |
+          echo "workspace"
+          ls ${{ github.workspace }}
+          echo "above"
+          ls ..
+          cd ../FAIR-CLI
+          poetry install
+          source .venv/bin/activate
+          cd ${{ github.workspace }}
+          fair init --using mac.yaml
+      - name: Install and initialise FAIR CLI
+        if: matrix.config.os == 'ubuntu-20.04'
+        run: |
+          echo "workspace"
+          ls ${{ github.workspace }}
+          echo "above"
+          ls ..
+          cd ../FAIR-CLI
+          poetry install
+          source .venv/bin/activate
+          cd ${{ github.workspace }}
+          fair init --using ubuntu.yaml
 
       - name: Install R API system requirements (macOS-latest)
         if: runner.os == 'macOS'
         run : |
               rm '/usr/local/bin/gfortran'
               brew install hdf5
               brew install gdal
-        shell: bash
       - name: Install R API system requirements (ubuntu-20.04)
         if: matrix.config.os == 'ubuntu-20.04'
         run: |
           while read -r cmd
           do
             eval sudo $cmd
           done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
-        shell: bash
-      - name: Install local registry
-        run: /bin/bash -c "$(curl -fsSL https://data.scrc.uk/static/localregistry.sh)"
-      - name: Start registry
-        run: $HOME/.fair/registry/scripts/start_fair_registry
 
       - name: Check
         env:

.github/workflows/test-coverage.yaml

@@ -40,6 +40,14 @@ jobs:
       - name: Start registry
         run: $HOME/.fair/registry/scripts/start_fair_registry
 
+      - name: init
+        run: |
+
+          rDataPipeline::fair_init(
+            name = "Sonia Mitchell",
+            identifier = "https://orcid.org/0000-0003-1536-2066",
+            endpoint = "http://localhost:8000/api/")
+        shell: Rscript {0}
       - name: Test coverage
         run: covr::codecov()
         shell: Rscript {0}

NAMESPACE

@@ -22,7 +22,6 @@ export(read_array)
 export(read_distribution)
 export(read_estimate)
 export(read_table)
-export(run_server)
 export(write_array)
 export(write_distribution)
 export(write_estimate)

R/download_data_product.R

@@ -19,8 +19,6 @@
 #'
 download_data_product <- function(data_product, version, namespace, data_dir) {
 
-  run_server()
-
   # Where is the file -------------------------------------------------------
 
   namespace_id <- get_entry("namespace", list(name = namespace))[[1]]$url %>%
@@ -38,8 +36,6 @@ download_data_product <- function(data_product, version, namespace, data_dir) {
   object <- get_entity(object_url)
   storage_location <- get_storage_location(object$storage_location)
 
-  stop_server()
-
   # Where should we save it -------------------------------------------------
 
   # If data_dir doesn't exist, create it

mac.yaml

@@ -0,0 +1,22 @@
+description: project
+git:
+  local_repo: /Users/Soniam/Desktop/git/FAIRDataPipeline/rFDP
+  remote: origin
+namespaces:
+  input: sonia
+  output: sonia
+registries:
+  local:
+    data_store: /Users/runner/.fair/data/
+    directory: /Users/runner/.fair/registry/
+    uri: http://localhost:8000/api/
+  origin:
+    data_store: https://data.scrc.uk/data/
+    token: ${{ github.workspace }}/token.txt
+    uri: https://data.scrc.uk/api/
+user:
+  email: sonia.mitchell@glasgow.ac.uk
+  family_name: Mitchell
+  given_names: Sonia
+  orcid: 0000-0003-1536-2066
+  uuid: 595638a0-fe69-4314-b108-3043b5785515

tests/testthat.R

@@ -4,9 +4,4 @@ library(rDataPipeline)
 Sys.setenv(FDP_endpoint = "http://localhost:8000/api/")
 endpoint <- Sys.getenv("FDP_endpoint")
 
-rDataPipeline::fair_init(
-  name = "Sonia Mitchell",
-  identifier = "https://orcid.org/0000-0003-1536-2066",
-  endpoint = endpoint)
-
 testthat::test_check("rDataPipeline")

token.txt

@@ -0,0 +1 @@
+58e60d4ae9521ff6373120b11679dbfebb6616f9

ubuntu.yaml

@@ -0,0 +1,22 @@
+description: project
+git:
+  local_repo: /Users/Soniam/Desktop/git/FAIRDataPipeline/rFDP
+  remote: origin
+namespaces:
+  input: sonia
+  output: sonia
+registries:
+  local:
+    data_store: /home/runner/.fair/data/
+    directory: /home/runner/.fair/registry/
+    uri: http://localhost:8000/api/
+  origin:
+    data_store: https://data.scrc.uk/data/
+    token: ${{ github.workspace }}/token.txt
+    uri: https://data.scrc.uk/api/
+user:
+  email: sonia.mitchell@glasgow.ac.uk
+  family_name: Mitchell
+  given_names: Sonia
+  orcid: 0000-0003-1536-2066
+  uuid: 595638a0-fe69-4314-b108-3043b5785515