add --container-engine option to cwl-docker-extract (#260)

Co-authored-by: Vasu Jaganath <vasu.jaganath@axleinfo.com>
PolusAI · Aug 16, 2024 · beefe05 · beefe05
1 parent b96d65d
commit beefe05
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Showing 3 changed files with 12 additions and 3 deletions.
diff --git a/src/sophios/api/pythonapi.py b/src/sophios/api/pythonapi.py
@@ -759,7 +759,10 @@ def run(self) -> None:
         # workflows, and if there is a local image available,
         # `docker run` will NOT query the remote repository for the latest image!
         # cwltool has a --force-docker-pull option, but this may cause multiple pulls in parallel.
-        cmd = ['cwl-docker-extract', '--force-download', f'autogenerated/{self.process_name}.cwl']
+        if args.container_engine == 'singularity':
+            cmd = ['cwl-docker-extract', f'-s --dir {args.homedir}', f'autogenerated/{self.process_name}.cwl']
+        else:
+            cmd = ['cwl-docker-extract', '--force-download', f'autogenerated/{self.process_name}.cwl']
         sub.run(cmd, check=True)
 
         # If you don't like it, you can programmatically overwrite anything in args

diff --git a/src/sophios/main.py b/src/sophios/main.py
@@ -191,7 +191,10 @@ def main() -> None:
         # workflows, and if there is a local image available,
         # `docker run` will NOT query the remote repository for the latest image!
         # cwltool has a --force-docker-pull option, but this may cause multiple pulls in parallel.
-        cmd = ['cwl-docker-extract', '--force-download', f'autogenerated/{yaml_stem}.cwl']
+        if args.container_engine == 'singularity':
+            cmd = ['cwl-docker-extract', f'-s --dir {args.homedir}', f'autogenerated/{yaml_stem}.cwl']
+        else:
+            cmd = ['cwl-docker-extract', '--force-download', f'autogenerated/{yaml_stem}.cwl']
         sub.run(cmd, check=True)
 
         if args.docker_remove_entrypoints:

diff --git a/tests/test_examples.py b/tests/test_examples.py
@@ -217,7 +217,10 @@ def run_workflows(yml_path_str: str, yml_path: Path, cwl_runner: str, args: argp
         # workflows, and if there is a local image available,
         # `docker run` will NOT query the remote repository for the latest image!
         # cwltool has a --force-docker-pull option, but this may cause multiple pulls in parallel.
-        cmd = ['cwl-docker-extract', '--force-download', f'autogenerated/{Path(yml_path).stem}.cwl']
+        if args.container_engine == 'singularity':
+            cmd = ['cwl-docker-extract', f'-s --dir {args.homedir}', f'autogenerated/{Path(yml_path).stem}.cwl']
+        else:
+            cmd = ['cwl-docker-extract', '--force-download', f'autogenerated/{Path(yml_path).stem}.cwl']
         sub.run(cmd, check=True)
 
         return