Initialise lab in payu checkout and Experiment() to check directory i…

…s writable

Checking base labdirectory for just write access fails for laboratory directories that don't exist yet.

payu/branch.py

@@ -22,20 +22,12 @@
 from payu.git_utils import GitRepository, git_clone, PayuBranchError
 
 LAB_WRITE_ACCESS_ERROR = """
-Do not have write access to the configured laboratory directory.
-Skipping creating metadata, setting up restart configuration, and archive/work
-symlinks.
-
-To fix the errors, edit one (or more) of the following config.yaml options that
-determine the laboratory path:
-    - 'laboratory': (Top-level directory for the model laboratory 
-        Default: /scratch/${PROJECT}/${USER}/${MODEL}
-    - 'shortpath' (Top-level directory for laboratory.
-        Default: /scratch/${PROJECT}
-    - 'project': (The project to use for payu PBS jobs. Default: ${PROJECT})
-
-Then either run 'payu setup' or rerun checkout command with the current git
-branch, e.g. `payu checkout -r  <RESTART_PATH> <CURRENT_BRANCH>`
+Failed to initialise laboratory directories. Skipping creating metadata,
+setting up restart configuration, and archive/work symlinks.
+
+To fix, first modify/remove the config.yaml options that determine laboratory
+path. Then either run 'payu setup' or rerun checkout command with the current
+git branch, e.g. `payu checkout -r  <RESTART_PATH> <CURRENT_BRANCH>`
 """
 
 NO_CONFIG_FOUND_MESSAGE = """No configuration file found on this branch.
@@ -138,15 +130,6 @@ def check_config_path(config_path: Optional[Path] = None) -> Optional[Path]:
     return config_path
 
 
-def check_laboratory_path(lab_basepath: str) -> None:
-    """Check if a laboratory path has write access"""
-    if not os.access(lab_basepath, os.W_OK | os.X_OK):
-        print(LAB_WRITE_ACCESS_ERROR)
-        raise PermissionError(
-            f"Laboratory directory does not have write access: {lab_basepath}"
-        )
-
-
 def checkout_branch(branch_name: str,
                     is_new_branch: bool = False,
                     is_new_experiment: bool = False,
@@ -198,7 +181,11 @@ def checkout_branch(branch_name: str,
 
     # Initialise Lab
     lab = Laboratory(model_type, config_path, lab_path)
-    check_laboratory_path(lab.basepath)
+    try:
+        lab.initialize()
+    except PermissionError:
+        print(LAB_WRITE_ACCESS_ERROR)
+        raise
 
     # Initialise metadata
     metadata = Metadata(Path(lab.archive_path),

payu/experiment.py

@@ -52,6 +52,8 @@ class Experiment(object):
 
     def __init__(self, lab, reproduce=False, force=False, metadata_off=False):
         self.lab = lab
+        # Check laboratory directories are writable
+        self.lab.initialize()
 
         if not force:
             # check environment for force flag under PBS

payu/laboratory.py

@@ -10,6 +10,17 @@
 
 from payu.fsops import mkdir_p, read_config
 
+LAB_INITIALIZE_ERROR = """
+The configured laboratory directory may not have write access. Edit/remove one
+(or more) of the following config.yaml options that determine the laboratory
+path:
+    - 'laboratory': Top-level directory for the model laboratory
+        Default: /scratch/${PROJECT}/${USER}/${MODEL}
+    - 'shortpath' Top-level directory for laboratory.
+        Default: /scratch/${PROJECT}
+    - 'project': The project to use for payu PBS jobs. Default: ${PROJECT}
+"""
+
 
 class Laboratory(object):
     """Interface to the numerical model's laboratory."""
@@ -84,7 +95,13 @@ def get_default_lab_path(self, config):
 
     def initialize(self):
         """Create the laboratory directories."""
-        mkdir_p(self.archive_path)
-        mkdir_p(self.bin_path)
-        mkdir_p(self.codebase_path)
-        mkdir_p(self.input_basepath)
+        try:
+            mkdir_p(self.archive_path)
+            mkdir_p(self.bin_path)
+            mkdir_p(self.codebase_path)
+            mkdir_p(self.input_basepath)
+        except PermissionError as e:
+            print(LAB_INITIALIZE_ERROR)
+            raise PermissionError(
+                f"Failed to initialise laboratory directories. Error: {e}"
+            )

test/test_branch.py

@@ -9,7 +9,6 @@
 
 from payu.branch import add_restart_to_config, check_restart, switch_symlink
 from payu.branch import checkout_branch, clone, list_branches
-from payu.branch import check_laboratory_path
 from payu.metadata import MetadataWarning
 from payu.fsops import read_config
 
@@ -515,20 +514,37 @@ def test_checkout_branch_with_restart_path(mock_uuid):
                           expected_parent_uuid=uuid1)
 
 
-@patch("os.access")
-def test_check_laboratory_path(mock_os_access):
-    # Test seems a bit useless as was unsure on how to create a directory
-    # without write permissions without locking myself out the directory
-    mock_os_access.return_value = False
+@patch("payu.laboratory.Laboratory.initialize")
+def test_checkout_laboratory_path_error(mock_lab_initialise):
+    mock_lab_initialise.side_effect = PermissionError
+
+    repo = setup_control_repository()
+    current_commit = repo.active_branch.object.hexsha
+
     with cd(ctrldir):
         # Test raises a permission error
         with pytest.raises(PermissionError):
-            check_laboratory_path("some/path")
+            checkout_branch(branch_name="Branch1",
+                            is_new_branch=True,
+                            lab_path=labdir)
+
+    # Assert new commit has not been added
+    assert repo.active_branch.object.hexsha == current_commit
 
-    mock_os_access.return_value = True
+    assert str(repo.active_branch) == "Branch1"
+    assert not (ctrldir / "metadata.yaml").exists()
+
+    # Test removing lab directory
+    shutil.rmtree(labdir)
+    mock_lab_initialise.side_effect = None
     with cd(ctrldir):
-        # Test check runs without errors
-        check_laboratory_path("some/path")
+        # Test runs without an error - directory is initialised
+        checkout_branch(branch_name="Branch2",
+                        is_new_branch=True,
+                        lab_path=labdir)
+
+    # Assert new commit has been added
+    assert repo.active_branch.object.hexsha != current_commit
 
 
 @patch("uuid.uuid4")