Move user membership in project tests to test_benchcab

benchcab/benchcab.py

@@ -64,15 +64,21 @@ def _validate_environment(self, project: str, modules: list):
             )
             sys.exit(1)
 
-        required_groups = [project, "ks32", "hh5"]
+        if project is None:
+            msg = """Couldn't resolve project: check 'project' in config.yaml
+                and/or $PROJECT set in ~/.config/gadi-login.conf
+                """
+            raise AttributeError(msg)
+
+        required_groups = set([project, "ks32", "hh5"])
         groups = [grp.getgrgid(gid).gr_name for gid in os.getgroups()]
-        if not set(required_groups).issubset(groups):
-            print(
-                "Error: user does not have the required group permissions.",
-                "The required groups are:",
-                ", ".join(required_groups),
+        if not required_groups.issubset(groups):
+            msg = (
+                f"""Error: user does not have the required group permissions.,
+                The required groups are:,
+                {", ".join(required_groups)}""",
             )
-            sys.exit(1)
+            raise PermissionError(msg)
 
         for modname in modules:
             if not self.modules_handler.module_is_avail(modname):

benchcab/config.py

@@ -83,27 +83,7 @@ def read_optional_key(config: dict):
         The configuration file with with/without optional keys
     """
     if "project" not in config:
-        if "PROJECT" not in os.environ:
-            msg = """Couldn't resolve project: check 'project' in config.yaml
-                and/or $PROJECT set in ~/.config/gadi-login.conf
-                """
-            raise ValueError(msg)
-        config["project"] = os.environ["PROJECT"]
-
-    groups = list(
-        set(
-            [
-                group
-                for data_dir in internal.USER_PROJECT_DIRS
-                for group in os.listdir(data_dir)
-            ]
-        )
-    )
-
-    if config["project"] not in groups:
-        msg = f"User is not a member of project [{config['project']}]: Check if project key is correct"
-
-        raise ValueError(msg)
+        config["project"] = os.environ.get("PROJECT", None)
 
     if "realisations" in config:
         for r in config["realisations"]:
@@ -166,8 +146,8 @@ def read_config(config_path: str) -> dict:
     """
     # Read configuration file
     config = read_config_file(config_path)
-    # Validate and return.
-    validate_config(config)
     # Populate configuration dict with optional keys
     read_optional_key(config)
+    # Validate and return.
+    validate_config(config)
     return config

benchcab/internal.py

@@ -28,10 +28,6 @@
 # Path to the user's current working directory
 CWD = Path.cwd()
 
-# Directory List is obtained from Gadi User Guide in Section - Gadi Resources
-# https://opus.nci.org.au/display/Help/0.+Welcome+to+Gadi
-USER_PROJECT_DIRS = ["/g/data", "/scratch"]
-
 # Path to the user's home directory
 HOME_DIR = Path(os.environ["HOME"])
 

docs/user_guide/config_options.md

@@ -32,8 +32,7 @@ The different running modes of `benchcab` are solely dependent on the options us
 
 ## project
 
-NCI project ID to charge the simulations to.
-This key is _optional_. If ID is not provided, the current workspace project - i.e. the environment variable `$PROJECT` will be used.
+: **Default:** user's default project, _optional key_. :octicons-dash-24: NCI project ID to charge the simulations to. The user's default project defined in the $PROJECT environment variable is used by default.
 
 ``` yaml
 

tests/test_benchcab.py

@@ -0,0 +1,67 @@
+"""`pytest` tests for `benchcab.py`."""
+import re
+from contextlib import nullcontext as does_not_raise
+from unittest import mock
+
+import pytest
+
+from benchcab.benchcab import Benchcab
+
+
+@pytest.fixture(scope="module", autouse=True)
+def _set_user_projects():
+    with mock.patch("grp.getgrgid") as mocked_getgrid, mock.patch(
+        "os.getgroups"
+    ) as mocked_groups:
+        type(mocked_getgrid.return_value).gr_name = mock.PropertyMock(
+            return_value="hh5"
+        )
+        mocked_groups.return_value = [1]
+        yield
+
+
+@pytest.fixture(scope="module", params=["hh5", "invalid_project_name"])
+def config_project(request):
+    """Get config project name."""
+    return request.param
+
+
+# Error message if config project name cannot be resolved.
+no_project_name_msg = re.escape(
+    """Couldn't resolve project: check 'project' in config.yaml
+       and/or $PROJECT set in ~/.config/gadi-login.conf
+    """
+)
+
+# For testing whether user is member of necessary projects to run benchcab, we need to simulate the environment of Gadi
+# TODO: Simulate Gadi environment for running tests for validating environment
+
+
+@pytest.mark.skip()
+@pytest.mark.parametrize(
+    ("config_project", "pytest_error"),
+    [
+        ("hh5", does_not_raise()),
+        (None, pytest.raises(AttributeError, match=no_project_name_msg)),
+    ],
+)
+def test_project_name(config_project, pytest_error):
+    """Tests whether config project name is suitable to run in Gadi environment."""
+    app = Benchcab(benchcab_exe_path=None)
+    with pytest_error:
+        app._validate_environment(project=config_project, modules=[])
+
+
+@pytest.mark.skip()
+@pytest.mark.parametrize(
+    ("config_project", "pytest_error"),
+    [
+        ("hh5", does_not_raise()),
+        ("invalid_project_name", pytest.raises(PermissionError)),
+    ],
+)
+def test_user_project_group(config_project, pytest_error):
+    """Test _validate_environment for if current user's groups does not contain the project name."""
+    app = Benchcab(benchcab_exe_path=None)
+    with pytest_error:
+        app._validate_environment(project=config_project, modules=[])

tests/test_config.py

@@ -17,16 +17,6 @@
 
 
 # Temporarily set $PROJECT for testing module
-@pytest.fixture(autouse=True, scope="module")
-def _set_project_validation_dirs():
-    with mock.patch("os.listdir") as mocked_listdir:
-        mocked_listdir.return_value = [
-            NO_OPTIONAL_CONFIG_PROJECT,
-            OPTIONAL_CONFIG_PROJECT,
-        ]
-        yield
-
-
 @pytest.fixture(autouse=True)
 def _set_project_env_variable(monkeypatch):
     # Clear existing environment variables first
@@ -162,6 +152,13 @@ def test_validate_config(config_str, pytest_error):
 class TestReadOptionalKey:
     """Tests related to adding optional keys in config."""
 
+    @pytest.fixture()
+    def all_optional_default_config_no_project(
+        self, all_optional_default_config
+    ) -> dict:
+        """Set project keyword to None."""
+        return all_optional_default_config | {"project": None}
+
     @pytest.mark.parametrize(
         ("input_config", "output_config"),
         [
@@ -176,28 +173,15 @@ def test_read_optional_key_add_data(self, input_config, output_config, request):
         bc.read_optional_key(config)
         assert pformat(config) == pformat(request.getfixturevalue(output_config))
 
-    def test_no_project_name(self, no_optional_config, monkeypatch):
+    def test_no_project_name(
+        self, no_optional_config, all_optional_default_config_no_project, monkeypatch
+    ):
         """If project key and $PROJECT are not provided, then raise error."""
         monkeypatch.delenv("PROJECT")
-        err_msg = re.escape(
-            """Couldn't resolve project: check 'project' in config.yaml
-                and/or $PROJECT set in ~/.config/gadi-login.conf
-            """
-        )
-        with pytest.raises(ValueError, match=err_msg):
-            bc.read_optional_key(no_optional_config)
-
-    def test_user_not_in_project(self, no_optional_config):
-        """If user is not in viewable NCI projects, raise error."""
-        no_optional_config["project"] = "non_existing"
-        err_msg = re.escape(
-            "User is not a member of project [non_existing]: Check if project key is correct"
+        bc.read_optional_key(no_optional_config)
+        assert pformat(no_optional_config) == pformat(
+            all_optional_default_config_no_project
         )
-        with pytest.raises(
-            ValueError,
-            match=err_msg,
-        ):
-            bc.read_optional_key(no_optional_config)
 
 
 @pytest.mark.parametrize(