Merge pull request #22 from workflowhub-eu/feature-docker-container

Feature docker container

.github/workflows/push-docker.yaml

@@ -0,0 +1,90 @@
+name: Docker
+
+on:
+  push:
+    branches: [ "develop" ]
+    # Publish semver tags as releases.
+    tags: [ 'v*.*.*' ]
+  pull_request:
+    branches: [ "develop" ]
+  workflow_dispatch:
+
+env:
+  REGISTRY: ghcr.io
+  ACTOR: OliverWoolland
+  IMAGE_NAME: ghcr.io/uomresearchit/workflowhub-graph
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      # This is used to complete the identity challenge
+      # with sigstore/fulcio when running outside of PRs.
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Install the cosign tool except on PR
+      # https://github.com/sigstore/cosign-installer
+      - name: Install cosign
+        if: github.event_name != 'pull_request'
+        uses: sigstore/cosign-installer@59acb6260d9c0ba8f4a2f9d9b48431a222b68e20 #v3.5.0
+        with:
+          cosign-release: 'v2.2.4'
+
+      # Set up BuildKit Docker container builder to be able to build
+      # multi-platform images and export cache
+      # https://github.com/docker/setup-buildx-action
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ env.ACTOR }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Extract metadata (tags, labels) for Docker
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0
+        with:
+          context: .
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      # Sign the resulting Docker image digest except on PRs.
+      # This will only write to the public Rekor transparency log when the Docker
+      # repository is public to avoid leaking data.  If you would like to publish
+      # transparency data even for private images, pass --force to cosign below.
+      # https://github.com/sigstore/cosign
+      - name: Sign the published Docker image
+        if: ${{ github.event_name != 'pull_request' }}
+        env:
+          # https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions#using-an-intermediate-environment-variable
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        # This step uses the identity token to provision an ephemeral certificate
+        # against the sigstore community Fulcio instance.
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}

Dockerfile

@@ -0,0 +1,25 @@
+# Docker container with poetry for python package management
+
+FROM python:3.10-slim
+
+# Install poetry
+RUN pip install poetry
+
+# Set the working directory
+WORKDIR /app
+
+# Copy the pyproject.toml
+COPY pyproject.toml /app/
+
+# Install the dependencies
+RUN poetry install --no-root
+
+# Copy the rest of the files
+COPY . /app
+
+# Install the package
+RUN poetry install
+
+# Run the application
+CMD ["help"]
+ENTRYPOINT ["poetry", "run"]

README.md

@@ -1,5 +1,38 @@
 # WorkflowHub Knowledge Graph 
 
+## Getting started
+
+### Obtaining workflowhub-graph
+
+workflowhub-graph is available packaged as a Docker container. You can pull the latest version of the container by running:
+
+```bash
+docker pull ghcr.io/uomresearchit/workflowhub-graph:latest
+```
+
+This provides the a wrapper for the executable `workflowhub-graph` which can be used to run the various tools provided by the package.
+
+### Running workflowhub-graph
+
+There are several tools provided by the `workflowhub-graph` package. These are:
+- 'help': Display help information.
+- 'source-crates': Download ROCrates from the WorkflowHub API.
+- 'absolutize': Make all paths in an ROCrate absolute.
+- 'upload': Upload an ROCrate to Zenodo.
+- 'merge': Merge multiple ROCrates into an RDF graph.
+
+To run any of these tools, you can use the following command:
+
+```bash
+docker run ghcr.io/uomresearchit/workflowhub-graph:latest <tool> <args>
+```
+
+For example, to download ROCrates from the WorkflowHub API, you can run:
+
+```bash
+docker run ghcr.io/uomresearchit/workflowhub-graph:latest source-crates
+```
+
 ## Contributing
 
 ### Coding Style

pyproject.toml

@@ -18,10 +18,11 @@ certifi = "^2024.2.2"
 pytest = ">=8.2.1"
 
 [tool.poetry.scripts]
-workflowhub-graph-source-crates = "workflowhub_graph.source_crates:main"
-workflowhub-graph-absolutize = "workflowhub_graph.absolutize:main"
-workflowhub-graph-merge = "workflowhub_graph.merge:main"
-workflowhub-graph-upload = "workflowhub_graph.upload:main"
+source-crates = "workflowhub_graph.source_crates:main"
+absolutize = "workflowhub_graph.absolutize:main"
+merge = "workflowhub_graph.merge:main"
+upload = "workflowhub_graph.upload:main"
+help = "workflowhub_graph.help:main"
 
 [tool.poetry.group.dev.dependencies]
 pytest = ">=8.2.1"

workflowhub_graph/help.py

@@ -0,0 +1,22 @@
+import argparse
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Provide help and examples for the workflowhub graph builder."
+    )
+    args = parser.parse_args()
+
+    # Print a list of poetry scripts
+    print(
+        """
+        The following commands are available:
+
+        - 'source-crates': Download ROCrates from the WorkflowHub API.
+        - 'absolutize': Make all paths in an ROCrate absolute.
+        - 'upload': Upload an ROCrate to Zenodo.
+        - 'merge': Merge multiple ROCrates into an RDF graph.
+        """
+    )
+
+if __name__ == "__main__":
+    main()