test: better test conditions

Author: natthan-pigoux

tests/test_singularity.py

@@ -175,7 +175,7 @@ def test_singularity_local_sandbox_image(tmp_path: Path):
             "singularity",
             "build",
             "--sandbox",
-            container_path / "alpine",
+            str(container_path / "alpine"),
             "docker://alpine:latest",
         ]
 
@@ -196,25 +196,35 @@ def test_singularity_local_sandbox_image(tmp_path: Path):
 
 
 @needs_singularity
-def test_singularity_inspect_image(tmp_path: Path):
+def test_singularity_inspect_image(tmp_path: Path, monkeypatch: pytest.MonkeyPatch):
     workdir = tmp_path / "working_dir"
     workdir.mkdir()
-    with working_directory(workdir):
-        # build a sandbox image
-        repo_path = workdir / "container_repo"
-        image_path = repo_path / "alpine"
-        res_inspect = _inspect_singularity_image(str(image_path))
-        assert res_inspect is False
-        repo_path.mkdir()
-        cmd = [
-            "singularity",
-            "build",
-            "--sandbox",
-            image_path,
-            "docker://alpine:latest",
-        ]
+    repo_path = workdir / "container_repo"
+    image_path = repo_path / "alpine"
+
+    # test path does not exists
+    res_inspect = _inspect_singularity_image(str(image_path))
+    assert res_inspect is False
+
+    # 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 container image
         res_inspect = _inspect_singularity_image(image_path)
         assert res_inspect is True
+
+    # test wrong subprocess call
+    def mock_failed_subprocess(*args, **kwargs):
+        raise subprocess.CalledProcessError(returncode=1, cmd=args[0])
+    
+    monkeypatch.setattr("cwltool.singularity.run", mock_failed_subprocess)
+    res_inspect = _inspect_singularity_image(str(image_path))
+    assert res_inspect is False

tests/test_tmpdir.py

@@ -324,39 +324,52 @@ def test_singularity_get_image_from_sandbox(monkeypatch: pytest.MonkeyPatch, tmp
 
     workdir = tmp_path / "working_dir"
     workdir.mkdir()
-    # build a sandbox image
     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)
-    assert not SingularityCommandLineJob(
+    req = {"class": "DockerRequirement", "dockerPull": f"{image_path}"}
+    res = SingularityCommandLineJob(
         builder, {}, CommandLineTool.make_path_mapper, [], [], ""
     ).get_image(
-        {
-            "class": "DockerRequirement",
-            "dockerPull": f"{image_path}",
-        },
+        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)
-    assert SingularityCommandLineJob(
+    req = {"class": "DockerRequirement", "dockerPull": f"{image_path}"}
+    res =  SingularityCommandLineJob(
         builder, {}, CommandLineTool.make_path_mapper, [], [], ""
     ).get_image(
-        {
-            "class": "DockerRequirement",
-            "dockerPull": f"{image_path}",
-        },
+        req,
+        pull_image=False,
+        tmp_outdir_prefix=str(tmp_outdir_prefix),
+        force_pull=False,
+    )
+    assert req["dockerPull"] == str(image_path)
+    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: