Do not require docker save

Author: jfennick

README.rst

@@ -49,15 +49,15 @@ the software container images in Docker format.
 
 .. code:: bash
 
-   cwl-docker-extract DIRECTORY path_to_my_workflow.cwl
+   cwl-docker-extract path_to_my_workflow.cwl
 
 Or you can use the Singularity software container engine to download and
 save the software container images and convert them to the Singularity
 format at the same time.
 
 .. code:: bash
 
-   cwl-docker-extract --singularity DIRECTORY path_to_my_workflow.cwl
+   cwl-docker-extract --singularity --dir DIRECTORY path_to_my_workflow.cwl
 
 
 Print all referenced software packages

cwl_utils/docker_extract.py

@@ -21,10 +21,10 @@ def arg_parser() -> argparse.ArgumentParser:
         description="Save container images specified in a CWL document (Workflow or CommandLineTool). "
         "For CWL Workflows, all steps will also be searched (recursively)."
     )
-    parser.add_argument("dir", help="Directory in which to save images")
     parser.add_argument(
         "input", help="Input CWL document (CWL Workflow or CWL CommandLineTool)"
     )
+    parser.add_argument("--dir", help="Directory in which to save images")
     parser.add_argument(
         "-s",
         "--singularity",
@@ -45,7 +45,12 @@ def arg_parser() -> argparse.ArgumentParser:
 
 def run(args: argparse.Namespace) -> List[cwl.DockerRequirement]:
     """Extract the docker reqs and download them using Singularity or Docker."""
-    os.makedirs(args.dir, exist_ok=True)
+    if args.singularity and not args.dir:
+        print("Error! Must specify --dir if using --singularity")
+        sys.exit(1)
+
+    if args.dir:
+        os.makedirs(args.dir, exist_ok=True)
 
     top = cwl.load_document_by_uri(args.input)
     reqs: List[cwl.DockerRequirement] = []

cwl_utils/image_puller.py

@@ -17,7 +17,11 @@
 
 class ImagePuller(ABC):
     def __init__(
-        self, req: str, save_directory: Union[str, Path], cmd: str, force_pull: bool
+        self,
+        req: str,
+        save_directory: Union[None, str, Path],
+        cmd: str,
+        force_pull: bool,
     ) -> None:
         """Create an ImagePuller."""
         self.req = req
@@ -62,22 +66,24 @@ def generate_udocker_loading_command(self) -> str:
 
     def save_docker_image(self) -> None:
         """Download and save the software container image to disk as a docker tarball."""
-        _LOGGER.info(f"Pulling {self.req} with Docker...")
+        _LOGGER.info(f"Pulling {self.req} with {self.cmd}...")
         cmd_pull = [self.cmd, "pull", self.req]
         ImagePuller._run_command_pull(cmd_pull)
-        dest = os.path.join(self.save_directory, self.get_image_name())
-        if self.force_pull:
-            os.remove(dest)
-        cmd_save = [
-            self.cmd,
-            "save",
-            "-o",
-            dest,
-            self.req,
-        ]
-        subprocess.run(cmd_save, check=True)  # nosec
-        _LOGGER.info(f"Image successfully pulled: {dest!r}.")
-        print(self.generate_udocker_loading_command())
+        _LOGGER.info(f"Image successfully pulled: {self.req}")
+        if self.save_directory:
+            dest = os.path.join(self.save_directory, self.get_image_name())
+            if self.save_directory and self.force_pull:
+                os.remove(dest)
+            cmd_save = [
+                self.cmd,
+                "save",
+                "-o",
+                dest,
+                self.req,
+            ]
+            subprocess.run(cmd_save, check=True)  # nosec
+            _LOGGER.info(f"Image successfully saved: {dest!r}.")
+            print(self.generate_udocker_loading_command())
 
 
 class SingularityImagePuller(ImagePuller):

tests/test_docker_extract.py

@@ -43,6 +43,7 @@ def test_container_extraction_force(engine: str, tmp_path: Path) -> None:
     """Test force pull container extraction."""
 
     args = [
+        "--dir",
         str(tmp_path),
         get_data("testdata/md5sum.cwl"),
         "--container-engine",
@@ -54,6 +55,7 @@ def test_container_extraction_force(engine: str, tmp_path: Path) -> None:
     assert len(reqs) == 1
     assert len(list(tmp_path.iterdir())) == 1
     args = [
+        "--dir",
         str(tmp_path),
         get_data("testdata/md5sum.cwl"),
         "--container-engine",
@@ -81,6 +83,7 @@ def test_container_extraction_no_dockerPull(
     """Test container extraction tool when dockerPull is missing."""
 
     args = [
+        "--dir",
         str(tmp_path),
         get_data("testdata/debian_image_id.cwl"),
         "--container-engine",
@@ -113,6 +116,7 @@ def test_container_extraction_embedded_step(engine: str, tmp_path: Path) -> None
     """Test container extraction tool."""
 
     args = [
+        "--dir",
         str(tmp_path),
         get_data("testdata/workflows/count-lines16-wf.cwl"),
         "--container-engine",