support colons in paths on Singularity 3.9+/Apptainer 1.0+

Author: mr-c

cwltool/docker.py

@@ -207,7 +207,13 @@ def get_from_requirements(
         raise WorkflowException("Docker image %s not found" % r["dockerImageId"])
 
     @staticmethod
-    def append_volume(runtime: List[str], source: str, target: str, writable: bool = False) -> None:
+    def append_volume(
+        runtime: List[str],
+        source: str,
+        target: str,
+        writable: bool = False,
+        skip_mkdirs: bool = False,
+    ) -> None:
         """Add binding arguments to the runtime list."""
         options = [
             "type=bind",
@@ -221,7 +227,7 @@ def append_volume(runtime: List[str], source: str, target: str, writable: bool =
         mount_arg = output.getvalue().strip()
         runtime.append(f"--mount={mount_arg}")
         # Unlike "--volume", "--mount" will fail if the volume doesn't already exist.
-        if not os.path.exists(source):
+        if (not skip_mkdirs) and (not os.path.exists(source)):
             os.makedirs(source)
 
     def add_file_or_directory_volume(

cwltool/singularity.py

@@ -13,6 +13,7 @@
 
 from .builder import Builder
 from .context import RuntimeContext
+from .docker import DockerCommandLineJob
 from .errors import WorkflowException
 from .job import ContainerCommandLineJob
 from .loghandler import _logger
@@ -106,6 +107,14 @@ def is_version_3_4_or_newer() -> bool:
     return v[0][0] >= 4 or (v[0][0] == 3 and v[0][1] >= 4)
 
 
+def is_version_3_9_or_newer() -> bool:
+    """Detect if Singularity v3.9+ is available."""
+    if is_apptainer_1_or_newer():
+        return True  # this is equivalent to singularity-ce > 3.9.5
+    v = get_version()
+    return v[0][0] >= 4 or (v[0][0] == 3 and v[0][1] >= 9)
+
+
 def _normalize_image_id(string: str) -> str:
     return string.replace("/", "_") + ".img"
 
@@ -297,13 +306,16 @@ def get_from_requirements(
     @staticmethod
     def append_volume(runtime: List[str], source: str, target: str, writable: bool = False) -> None:
         """Add binding arguments to the runtime list."""
-        runtime.append("--bind")
-        # Mounts are writable by default, so 'rw' is optional and not
-        # supported (due to a bug) in some 3.6 series releases.
-        vol = f"{source}:{target}"
-        if not writable:
-            vol += ":ro"
-        runtime.append(vol)
+        if is_version_3_9_or_newer():
+            DockerCommandLineJob.append_volume(runtime, source, target, writable, skip_mkdirs=True)
+        else:
+            runtime.append("--bind")
+            # Mounts are writable by default, so 'rw' is optional and not
+            # supported (due to a bug) in some 3.6 series releases.
+            vol = f"{source}:{target}"
+            if not writable:
+                vol += ":ro"
+            runtime.append(vol)
 
     def add_file_or_directory_volume(
         self, runtime: List[str], volume: MapperEnt, host_outdir_tgt: Optional[str]

cwltool/udocker.py

@@ -9,6 +9,12 @@ class UDockerCommandLineJob(DockerCommandLineJob):
     """Runs a CommandLineJob in a software container using the udocker engine."""
 
     @staticmethod
-    def append_volume(runtime: List[str], source: str, target: str, writable: bool = False) -> None:
+    def append_volume(
+        runtime: List[str],
+        source: str,
+        target: str,
+        writable: bool = False,
+        skip_mkdirs: bool = False,
+    ) -> None:
         """Add binding arguments to the runtime list."""
         runtime.append("--volume={}:{}:{}".format(source, target, "rw" if writable else "ro"))

tests/test_environment.py

@@ -28,7 +28,7 @@ def assert_envvar_matches(check: CheckerTypes, k: str, env: Mapping[str, str]) -
         if isinstance(check, str):
             assert v == check, f"Environment variable {k} == {v!r} != {check!r}"
         else:
-            assert check(v, env), f"Environment variable {k}={v!r} fails check"
+            assert check(v, env), f"Environment variable {k}={v!r} fails check."
 
 
 def assert_env_matches(
@@ -149,11 +149,14 @@ def PWD(v: str, env: Env) -> bool:
         elif vminor > 5:
             sing_vars["SINGULARITY_COMMAND"] = "exec"
             if vminor >= 7:
+                if vminor > 9:
+                    sing_vars["SINGULARITY_BIND"] = ""
+                else:
 
-                def BIND(v: str, env: Env) -> bool:
-                    return v.startswith(tmp_prefix) and v.endswith(":/tmp")
+                    def BIND(v: str, env: Env) -> bool:
+                        return v.startswith(tmp_prefix) and v.endswith(":/tmp")
 
-                sing_vars["SINGULARITY_BIND"] = BIND
+                    sing_vars["SINGULARITY_BIND"] = BIND
 
         result.update(sing_vars)
 

tests/util.py

@@ -152,13 +152,13 @@ def get_tool_env(
         args.append(inputs_file)
 
     with working_directory(tmp_path):
-        rc, stdout, _ = get_main_output(
+        rc, stdout, stderr = get_main_output(
             args,
             replacement_env=replacement_env,
             extra_env=extra_env,
             monkeypatch=monkeypatch,
         )
-        assert rc == 0
+        assert rc == 0, stdout + "\n" + stderr
 
         output = json.loads(stdout)
         with open(output["env"]["path"]) as _: