Merge pull request #353 from iishiishii/main

Add separate Zenodo upload workflow for testing

.github/workflows/publish-doi.py

@@ -18,12 +18,14 @@ def upload_container(container_filepath, container_name, token):
     # Upload the simg container to bucket in the created deposition
     # The target URL is a combination of the bucket link with the desired filename
     # seperated by a slash.
+    print("Uploading container to Zenodo...", container_filepath, os.path.basename(container_filepath))
     with open(container_filepath, "rb") as fp:
         r = requests.put(
             "%s/%s" % (bucket_url, os.path.basename(container_filepath)), # bucket is a flat structure, can't include subfolders in it
             data=fp,
             params=params,
         )
+    print("Upload", r.json())
 
     # Update the metadata
     data = {
@@ -43,6 +45,7 @@ def upload_container(container_filepath, container_name, token):
     # Publish the deposition
     r = requests.post('https://sandbox.zenodo.org/api/deposit/depositions/%s/actions/publish' % deposition_id,
                       params=params )
+    print("Publish", r.json())
 
     # Get the DOI from the deposition
     r = requests.get('https://sandbox.zenodo.org/api/deposit/depositions/%s' % deposition_id,

.github/workflows/test-zenodo-workflow.yml

@@ -0,0 +1,27 @@
+name: Update neurocontainers
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+
+jobs:
+  upload_containers_simg:
+    runs-on: self-hosted
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        token: ${{ secrets.ACCESS_TOKEN }}
+    - uses: actions/setup-python@v5
+      with:
+        python-version: 3.8
+    - name : Check if singularity container files exist in nectar cloud and build & upload if not there
+      run: |
+        IMAGE_HOME=/home/runner
+        IMAGENAME_BUILDDATE=dicomtools_1.0.0_20250204
+        echo "[DEBUG] ${IMAGENAME_BUILDDATE}.simg exists in temporary cache on nectar cloud"
+        curl --output "$IMAGE_HOME/${IMAGENAME_BUILDDATE}.simg" "https://object-store.rc.nectar.org.au/v1/AUTH_dead991e1fa847e3afcca2d3a7041f5d/neurodesk/temporary-builds-new/${IMAGENAME_BUILDDATE}.simg"
+        echo "Upload container $IMAGE_HOME/${IMAGENAME_BUILDDATE}.simg to Zenodo"
+        echo $(find $IMAGE_HOME/${IMAGENAME_BUILDDATE}.simg)
+        export DOI_URL=$(python3 .github/workflows/publish-doi.py --container_filepath="$IMAGE_HOME/${IMAGENAME_BUILDDATE}.simg" --container_name=${IMAGENAME_BUILDDATE} --token=${{ secrets.ZENODO_TOKEN }})