feat: handle singularity/apptainer sandbox images

cwltool/singularity.py

@@ -1,15 +1,17 @@
 """Support for executing Docker format containers using Singularity {2,3}.x or Apptainer 1.x."""
 
+import json
 import logging
 import os
 import os.path
 import re
 import shutil
 import sys
 from collections.abc import Callable, MutableMapping
-from subprocess import check_call, check_output  # nosec
+from subprocess import check_call, check_output, run  # nosec
 from typing import cast
 
+from mypy_extensions import mypyc_attr
 from schema_salad.sourceline import SourceLine
 from spython.main import Client
 from spython.main.parse.parsers.docker import DockerParser
@@ -145,6 +147,30 @@ def _normalize_sif_id(string: str) -> str:
     return string.replace("/", "_") + ".sif"
 
 
+@mypyc_attr(allow_interpreted_subclasses=True)
+def _inspect_singularity_image(path: str) -> bool:
+    """Inspect singularity image to be sure it is not an empty directory."""
+    cmd = [
+        "singularity",
+        "inspect",
+        "--json",
+        path,
+    ]
+    try:
+        result = run(cmd, capture_output=True, text=True)  # nosec
+    except Exception:
+        return False
+
+    if result.returncode == 0:
+        try:
+            output = json.loads(result.stdout)
+        except json.JSONDecodeError:
+            return False
+        if output.get("data", {}).get("attributes", {}):
+            return True
+    return False
+
+
 class SingularityCommandLineJob(ContainerCommandLineJob):
     def __init__(
         self,
@@ -229,6 +255,16 @@ def get_image(
                     )
                 found = True
         elif "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement:
+            # looking for local singularity sandbox image and handle it as a local image
+            if os.path.isdir(dockerRequirement["dockerPull"]) and _inspect_singularity_image(
+                dockerRequirement["dockerPull"]
+            ):
+                dockerRequirement["dockerImageId"] = dockerRequirement["dockerPull"]
+                _logger.info(
+                    "Using local Singularity sandbox image found in %s",
+                    dockerRequirement["dockerImageId"],
+                )
+                return True
             match = re.search(pattern=r"([a-z]*://)", string=dockerRequirement["dockerPull"])
             img_name = _normalize_image_id(dockerRequirement["dockerPull"])
             candidates.append(img_name)
@@ -243,6 +279,15 @@ def get_image(
         elif "dockerImageId" in dockerRequirement:
             if os.path.isfile(dockerRequirement["dockerImageId"]):
                 found = True
+            # handling local singularity sandbox image
+            elif os.path.isdir(dockerRequirement["dockerImageId"]) and _inspect_singularity_image(
+                dockerRequirement["dockerImageId"]
+            ):
+                _logger.info(
+                    "Using local Singularity sandbox image found in %s",
+                    dockerRequirement["dockerImageId"],
+                )
+                return True
             candidates.append(dockerRequirement["dockerImageId"])
             candidates.append(_normalize_image_id(dockerRequirement["dockerImageId"]))
             if is_version_3_or_newer():

tests/sing_local_sandbox_img_id_test.cwl

@@ -0,0 +1,14 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerImageId: container_repo/alpine
+
+inputs:
+  message: string
+
+outputs: []
+
+baseCommand: echo

tests/sing_local_sandbox_test.cwl

@@ -0,0 +1,14 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: container_repo/alpine
+
+inputs:
+  message: string
+
+outputs: []
+
+baseCommand: echo

tests/test_singularity.py

@@ -1,11 +1,17 @@
 """Tests to find local Singularity image."""
 
+import json
 import shutil
+import subprocess
+from collections.abc import Callable
 from pathlib import Path
+from typing import Any
 
 import pytest
+from mypy_extensions import KwArg, VarArg
 
 from cwltool.main import main
+from cwltool.singularity import _inspect_singularity_image
 
 from .util import (
     get_data,
@@ -159,3 +165,124 @@ def test_singularity3_docker_image_id_in_tool(tmp_path: Path) -> None:
             ]
         )
         assert result_code1 == 0
+
+
+@needs_singularity
+def test_singularity_local_sandbox_image(tmp_path: Path) -> None:
+    workdir = tmp_path / "working_dir"
+    workdir.mkdir()
+    with working_directory(workdir):
+        # build a sandbox image
+        container_path = workdir / "container_repo"
+        container_path.mkdir()
+        cmd = [
+            "singularity",
+            "build",
+            "--sandbox",
+            str(container_path / "alpine"),
+            "docker://alpine:latest",
+        ]
+
+        build = subprocess.run(cmd, capture_output=True, text=True)
+        if build.returncode == 0:
+            result_code, stdout, stderr = get_main_output(
+                [
+                    "--singularity",
+                    "--disable-pull",
+                    get_data("tests/sing_local_sandbox_test.cwl"),
+                    "--message",
+                    "hello",
+                ]
+            )
+            assert result_code == 0
+            result_code, stdout, stderr = get_main_output(
+                [
+                    "--singularity",
+                    "--disable-pull",
+                    get_data("tests/sing_local_sandbox_img_id_test.cwl"),
+                    "--message",
+                    "hello",
+                ]
+            )
+            assert result_code == 0
+        else:
+            pytest.skip(f"Failed to build the singularity image: {build.stderr}")
+
+
+@needs_singularity
+def test_singularity_inspect_image(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
+    """Test inspect a real image works."""
+    workdir = tmp_path / "working_dir"
+    workdir.mkdir()
+    repo_path = workdir / "container_repo"
+    image_path = repo_path / "alpine"
+
+    # test image exists
+    repo_path.mkdir()
+    cmd = [
+        "singularity",
+        "build",
+        "--sandbox",
+        str(image_path),
+        "docker://alpine:latest",
+    ]
+    build = subprocess.run(cmd, capture_output=True, text=True)
+    if build.returncode == 0:
+        # Verify the path is a correct container image
+        res_inspect = _inspect_singularity_image(str(image_path))
+        assert res_inspect is True
+    else:
+        pytest.skip(f"singularity sandbox image build didn't worked: {build.stderr}")
+
+
+class _DummyResult:  # noqa: B903
+    def __init__(self, rc: int, out: str) -> None:
+        self.returncode = rc
+        self.stdout = out
+
+
+def _make_run_result(
+    returncode: int, stdout: str
+) -> Callable[[VarArg(Any), KwArg(Any)], _DummyResult]:
+    """Mock subprocess.run returning returncode and stdout."""
+
+    def _runner(*args: Any, **kwargs: Any) -> _DummyResult:
+        return _DummyResult(returncode, stdout)
+
+    return _runner
+
+
+def test_json_decode_error_branch(monkeypatch: pytest.MonkeyPatch) -> None:
+    """Test json can't decode inspect result."""
+    monkeypatch.setattr("cwltool.singularity.run", _make_run_result(0, "not-a-json"))
+
+    def _raise_json_error(s: str) -> None:
+        # construct and raise an actual JSONDecodeError
+        raise json.JSONDecodeError("Expecting value", s, 0)
+
+    monkeypatch.setattr("json.loads", _raise_json_error)
+
+    assert _inspect_singularity_image("/tmp/image") is False
+
+
+def test_singularity_sandbox_image_not_exists() -> None:
+    image_path = "/tmp/not_existing/image"
+    res_inspect = _inspect_singularity_image(image_path)
+    assert res_inspect is False
+
+
+def test_singularity_sandbox_not_an_image(tmp_path: Path) -> None:
+    image_path = tmp_path / "image"
+    image_path.mkdir()
+    res_inspect = _inspect_singularity_image(str(image_path))
+    assert res_inspect is False
+
+
+def test_inspect_image_wrong_sb_call(monkeypatch: pytest.MonkeyPatch) -> None:
+
+    def mock_failed_subprocess(*args: Any, **kwargs: Any) -> None:
+        raise subprocess.CalledProcessError(returncode=1, cmd=args[0])
+
+    monkeypatch.setattr("cwltool.singularity.run", mock_failed_subprocess)
+    res_inspect = _inspect_singularity_image("/tmp/container_repo/alpine")
+    assert res_inspect is False

tests/test_tmpdir.py

@@ -285,6 +285,99 @@ def test_dockerfile_singularity_build(monkeypatch: pytest.MonkeyPatch, tmp_path:
     shutil.rmtree(subdir)
 
 
+@needs_singularity
+def test_singularity_get_image_from_sandbox(
+    monkeypatch: pytest.MonkeyPatch, tmp_path: Path
+) -> None:
+    """Test that SingularityCommandLineJob.get_image correctly handle sandbox image."""
+
+    (tmp_path / "out").mkdir(exist_ok=True)
+    tmp_outdir_prefix = tmp_path / "out"
+    tmp_outdir_prefix.mkdir(exist_ok=True)
+    (tmp_path / "tmp").mkdir(exist_ok=True)
+    tmpdir_prefix = str(tmp_path / "tmp")
+    runtime_context = RuntimeContext(
+        {"tmpdir_prefix": tmpdir_prefix, "user_space_docker_cmd": None}
+    )
+    builder = Builder(
+        {},
+        [],
+        [],
+        {},
+        schema.Names(),
+        [],
+        [],
+        {},
+        None,
+        None,
+        StdFsAccess,
+        StdFsAccess(""),
+        None,
+        0.1,
+        True,
+        False,
+        False,
+        "no_listing",
+        runtime_context.get_outdir(),
+        runtime_context.get_tmpdir(),
+        runtime_context.get_stagedir(),
+        INTERNAL_VERSION,
+        "singularity",
+    )
+
+    workdir = tmp_path / "working_dir"
+    workdir.mkdir()
+    repo_path = workdir / "container_repo"
+    repo_path.mkdir()
+    image_path = repo_path / "alpine"
+    image_path.mkdir()
+
+    # directory exists but is not an image
+    monkeypatch.setattr(
+        "cwltool.singularity._inspect_singularity_image", lambda *args, **kwargs: False
+    )
+    req = {"class": "DockerRequirement", "dockerPull": f"{image_path}"}
+    res = SingularityCommandLineJob(
+        builder, {}, CommandLineTool.make_path_mapper, [], [], ""
+    ).get_image(
+        req,
+        pull_image=False,
+        tmp_outdir_prefix=str(tmp_outdir_prefix),
+        force_pull=False,
+    )
+    assert req["dockerPull"].startswith("docker://")
+    assert res is False
+
+    # directory exists and is an image:
+    monkeypatch.setattr(
+        "cwltool.singularity._inspect_singularity_image", lambda *args, **kwargs: True
+    )
+    req = {"class": "DockerRequirement", "dockerPull": f"{image_path}"}
+    res = SingularityCommandLineJob(
+        builder, {}, CommandLineTool.make_path_mapper, [], [], ""
+    ).get_image(
+        req,
+        pull_image=False,
+        tmp_outdir_prefix=str(tmp_outdir_prefix),
+        force_pull=False,
+    )
+    assert req["dockerImageId"] == str(image_path)
+    assert res
+
+    # test that dockerImageId is set and image exists:
+    req = {"class": "DockerRequirement", "dockerImageId": f"{image_path}"}
+    res = SingularityCommandLineJob(
+        builder, {}, CommandLineTool.make_path_mapper, [], [], ""
+    ).get_image(
+        req,
+        pull_image=False,
+        tmp_outdir_prefix=str(tmp_outdir_prefix),
+        force_pull=False,
+    )
+    assert req["dockerImageId"] == str(image_path)
+    assert res
+
+
 def test_docker_tmpdir_prefix(tmp_path: Path) -> None:
     """Test that DockerCommandLineJob respects temp directory directives."""
     (tmp_path / "3").mkdir()