Automatically generate Docker label for XNAT container service as par…

…t of the GitHub build

.github/workflows/docker_publish.yml

@@ -44,9 +44,8 @@ jobs:
                       command_list.append(command_string)
 
           commands = ','.join(command_list)
-          label = f'org.nrg.commands=[{commands}]'
           with open(os.environ['GITHUB_OUTPUT'], 'a') as github_output:
-              print(f"label={label}", file=github_output)
+              print(f"nrglabel=[{commands}]", file=github_output)
         shell: python
 
       # Log into the container registry
@@ -59,22 +58,22 @@ jobs:
 
       # Extract metadata (tags and labels) to be applied to the image. See [docker/metadata-action](https://github.com/docker/metadata-action#about)
       # The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
+      # The current version does not allow for labels to be added containing the # symbol, so we add the
+      # custom nrg label in the build-push-action below
       - name: Extract metadata for Docker
         id: meta
         uses: docker/metadata-action@v5
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
-          #          labels: |
-          #            # set xnat container service label defining commands in this image
-          #            ${{ steps.xnat-command-label.outputs.label }}
+          # labels: 'org.nrg.commands=${{ steps.xnat-command-label.outputs.nrglabel }}'
           tags: |
             # set latest tag for default branch
             type=raw,value=latest,enable={{is_default_branch}}
 
       # Build the image from the Dockerfile in the repo and push to the container registry.
       # The `context` parameter defines the build's context as the set of files located in the
-      # specified path. For more information, see
-      # "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the
+      # specified path. For more information,
+      # see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the
       # `docker/build-push-action` repository.
       # Tag and label the image using the output from the metadata step above
       - name: Build and push Docker image
@@ -84,4 +83,6 @@ jobs:
           context: .
           push: true
           tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
+          labels: |
+            ${{ steps.meta.outputs.labels }}
+            org.nrg.commands=${{ steps.xnat-command-label.outputs.nrglabel }}

Dockerfile

@@ -23,5 +23,3 @@ ENV PATH=/opt/venv/bin:$PATH
 
 # Default command to execute
 CMD ["share-to-genetic"]
-
-LABEL org.nrg.commands="[{\"name\": \"share-to-genetic\", \"description\": \"Share subject to genetic project\", \"label\": \"Share subject to genetic project\", \"version\": \"1.0\", \"schema-version\": \"1.0\", \"type\": \"docker\", \"command-line\": \"share_subject_to_genetic_project #SUBJECTID#\", \"image\": \"ghcr.io/ucl-mirsg/drc-containers:latest\", \"override-entrypoint\": true, \"mounts\": [], \"inputs\": [{\"name\": \"SUBJECTID\", \"description\": \"The subject ID\", \"type\": \"string\", \"user-settable\": false, \"required\": true, \"replacement-key\": \"#SUBJECTID#\"}], \"outputs\": [], \"xnat\": [{\"name\": \"share-subject-to-genetic\", \"label\": \"Share subject to genetic project\", \"description\": \"Shares subject to the corresponding genetic project\", \"contexts\": [\"xnat:subjectData\"], \"external-inputs\": [{\"name\": \"subject\", \"description\": \"Input subject\", \"type\": \"Subject\", \"required\": true, \"load-children\": false}], \"derived-inputs\": [{\"name\": \"subject-id\", \"type\": \"string\", \"derived-from-wrapper-input\": \"subject\", \"derived-from-xnat-object-property\": \"id\", \"provides-value-for-command-input\": \"SUBJECTID\", \"user-settable\": false, \"required\": true}], \"output-handlers\": []}]}]"

README.md

@@ -23,6 +23,7 @@ array and the first argument is the function being executed
 
 If you need to add additional python module dependencies, you will need to
 configure these in `pyproject.toml` in the `[project]` section, e.g.:
+
 ```toml
 [project]
 dependencies = [
@@ -70,14 +71,22 @@ your container.
   [XNAT documentation](https://wiki.xnat.org/container-service/json-command-definition)
   for full details.
 
-### 4. Run `generate_docker_label.py`
+### 4. Commit and push the changes to the repository
+
+GitHub actions will build and publish the Docker image, and create the
+`org.nrg.commands` Docker label using the json command definition files in the
+repository.
 
-This generates a Docker label for the XNAT container service.
+### For local testing: `generate_docker_label.py`
 
-Add this to the end of the Dockerfile (including the `LABEL` statement and
-replacing any existing label).
+This script generates a Docker label for the XNAT constainer service which is
+equivalent to the one created by the GitHub Actions workflow. You do not need to
+run this script unless you wish to do so for testing purposes.
 
-### 5. Commit and push the changes to the repository
+If you wish to add this label to your local docker image, you can add this to
+the end of your Dockerfile (including the `LABEL` statement and replacing any
+existing label). However, you should not check the label into the repository
+since the label is generated by the GitHub Actions workflow.
 
 ---
 

generate_docker_label.py

@@ -34,7 +34,10 @@ def main():
             with open(file) as f:
                 command_object = json.load(f)
                 command_string = (
-                    json.dumps(command_object).replace('"', r"\"").replace("$", r"\$")
+                    json.dumps(command_object)
+                    .replace("\\", "\\\\")
+                    .replace('"', '\\"')
+                    .replace("$", "\\$")
                 )
                 command_list.append(command_string)