[feat] : re-add syncing workflow (#53)

* add option to not output csv file

* add workflow

.github/workflows/sync-to-portal.yml

@@ -0,0 +1,31 @@
+name: Sync manifests to portal tables
+
+on:
+  workflow_dispatch:
+
+jobs:
+  update:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: portal_tables
+    steps:
+    - uses: actions/[email protected]
+
+    - name: Setup Python
+      uses: actions/[email protected]
+      with:
+        python-version: '3.12'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install synapseclient pandas
+
+    - name: Sync to portal
+      run: |
+        python sync_publications.py --noprint
+        python sync_datasets.py --noprint
+        python sync_tools.py --noprint
+      env: 
+        SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_AUTH_TOKEN }}

portal_tables/sync_datasets.py

@@ -129,8 +129,9 @@ def main():
         utils.update_table(syn, args.portal_table_id, final_database)
         print()
 
-    print(f"📄 Saving copy of final table to: {args.output_csv}...")
-    final_database.to_csv(args.output_csv, index=False)
+    if not args.noprint:
+        print(f"📄 Saving copy of final table to: {args.output_csv}...")
+        final_database.to_csv(args.output_csv, index=False)
     print("\n\nDONE ✅")
 
 

portal_tables/sync_education.py

@@ -85,8 +85,9 @@ def main():
         utils.update_table(syn, args.portal_table_id, final_database)
         print()
 
-    print(f"📄 Saving copy of final table to: {args.output_csv}...")
-    final_database.to_csv(args.output_csv, index=False)
+    if not args.noprint:
+        print(f"📄 Saving copy of final table to: {args.output_csv}...")
+        final_database.to_csv(args.output_csv, index=False)
     print("\n\nDONE ✅")
 
 

portal_tables/sync_grants.py

@@ -81,8 +81,9 @@ def main():
         utils.update_table(syn, args.portal_table_id, final_database)
         print()
 
-    print(f"📄 Saving copy of final table to: {args.output_csv}...")
-    final_database.to_csv(args.output_csv, index=False)
+    if not args.noprint:
+        print(f"📄 Saving copy of final table to: {args.output_csv}...")
+        final_database.to_csv(args.output_csv, index=False)
     print("\n\nDONE ✅")
 
 

portal_tables/sync_people.py

@@ -102,8 +102,9 @@ def main():
         utils.update_table(syn, args.portal_table_id, final_database)
         print()
 
-    print(f"📄 Saving copy of final table to: {args.output_csv}...")
-    final_database.to_csv(args.output_csv, index=False)
+    if not args.noprint:
+        print(f"📄 Saving copy of final table to: {args.output_csv}...")
+        final_database.to_csv(args.output_csv, index=False)
     print("\n\nDONE ✅")
 
 

portal_tables/sync_publications.py

@@ -119,8 +119,9 @@ def main():
         utils.update_table(syn, args.portal_table_id, final_database)
         print()
 
-    print(f"📄 Saving copy of final table to: {args.output_csv}...")
-    final_database.to_csv(args.output_csv, index=False)
+    if not args.noprint:
+        print(f"📄 Saving copy of final table to: {args.output_csv}...")
+        final_database.to_csv(args.output_csv, index=False)
     print("\n\nDONE ✅")
 
 

portal_tables/sync_tools.py

@@ -119,8 +119,9 @@ def main():
         utils.update_table(syn, args.portal_table_id, final_database)
         print()
 
-    print(f"📄 Saving copy of final table to: {args.output_csv}...")
-    final_database.to_csv(args.output_csv, index=False)
+    if not args.noprint:
+        print(f"📄 Saving copy of final table to: {args.output_csv}...")
+        final_database.to_csv(args.output_csv, index=False)
     print("\n\nDONE ✅")
 
 

portal_tables/utils.py

@@ -69,6 +69,12 @@ def get_args(resource: str) -> argparse.Namespace:
         action="store_true",
         help="Output all logs and interim tables.",
     )
+    parser.add_argument(
+        "-np",
+        "--noprint",
+        action="store_true",
+        help="Do not output CSV file.",
+    )
     return parser.parse_args()