Merge pull request #358 from iishiishii/main

Remove Zenodo doi creation from update neurocontainer action

.github/workflows/update-neurocontainers.yml

@@ -22,7 +22,7 @@ jobs:
         python-version: 3.8
     - name : Check if singularity container files exist in nectar cloud and build & upload if not there
       run: |
-        /bin/bash .github/workflows/upload_containers_simg.sh ${{ secrets.ZENODO_TOKEN }}
+        /bin/bash .github/workflows/upload_containers_simg.sh
     - name: Auto commit changes to applist.json
       uses: stefanzweifel/git-auto-commit-action@v4
       id: auto-commit-action

.github/workflows/upload_containers_simg.sh

@@ -44,8 +44,6 @@ do
             # download simg file from cache:
             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"
-            export DOI_URL=$(python3 .github/workflows/publish-doi.py --container_filepath="$IMAGE_HOME/${IMAGENAME_BUILDDATE}.simg" --container_name=${IMAGENAME_BUILDDATE} --token=$1)
             echo "[DEBUG] Deleting file after download or when older than 30days from cache ..."
             rclone delete nectar:/neurodesk/temporary-builds-new/${IMAGENAME_BUILDDATE}.simg
             rclone delete --min-age 30d nectar:/neurodesk/temporary-builds-new
@@ -106,7 +104,7 @@ mv log.txt cvmfs
 
 cd cvmfs
 echo "[Debug] generate applist.json file for website"
-python json_gen.py --application=$IMAGENAME_BUILDDATE --doi_url=$DOI_URL #this generates the applist.json for the website
+python json_gen.py #this generates the applist.json for the website
 # these files will be committed via uses: stefanzweifel/git-auto-commit-action@v4
 
 

cvmfs/json_gen.py

@@ -1,31 +1,17 @@
 import json
-import argparse
 
-def process_text_to_json(application, doi_url):
+def process_text_to_json():
     my_dict = {}
     val = []
 
     with open("log.txt") as f:
         for line in f:
             line = line.split()
-
-            # Find the matching application and update its DOI
-            if application in line[0]:
-                val.append({"application": line[0], "categories": ' '.join(line[1:]).replace("categories:","").rstrip(',').split(","), "doi": doi_url})
-            else:
-                val.append({"application": line[0], "categories": ' '.join(line[1:]).replace("categories:","").rstrip(',').split(",")})
+            val.append({"application": line[0], "categories": ' '.join(line[1:]).replace("categories:","").rstrip(',').split(",")})
         my_dict['list'] = val
 
     with open('applist.json', 'w') as fp:     
         json.dump(my_dict, fp, sort_keys=True, indent=4)
 
 if __name__ == '__main__':
-    parser = argparse.ArgumentParser(
-        prog="Update DOI for app list",
-    )
-    parser.add_argument("--application", type=str, required=True, help="Application name and version")
-    parser.add_argument("--doi_url", type=str, required=True, help="DOI URL")
-
-    args = parser.parse_args()
-
-    process_text_to_json(args.application, args.doi_url)
+    process_text_to_json()