Merge remote-tracking branch 'origin/main' into 23-e4edm-results-in-e…

…rror-thrown

e4e_data_management/core.py

@@ -93,7 +93,7 @@ def initialize_dataset(self, date: dt.date, project: str, location: str, directo
             raise RuntimeError('Dataset with that name already exists!')
 
         self.active_dataset = Dataset(
-            root=dataset_path.absolute(),
+            root=dataset_path.resolve(),
             day_0=date
         )
         self.active_dataset.create()
@@ -127,7 +127,7 @@ def status(self) -> str:
         output = ''
         if self.active_dataset:
             name = self.active_dataset.name
-            path = self.active_dataset.root.absolute().as_posix()
+            path = self.active_dataset.root.resolve().as_posix()
             output += f'Dataset {name} at {path} activated'
         else:
             output += 'No dataset active'
@@ -136,7 +136,7 @@ def status(self) -> str:
         output += '\n'
         if self.active_mission:
             name = self.active_mission.name
-            path = self.active_mission.path.absolute().as_posix()
+            path = self.active_mission.path.resolve().as_posix()
             output += f'Mission {name} at {path} activated'
         else:
             output += 'No mission active'
@@ -147,9 +147,13 @@ def status(self) -> str:
             output += f'{len(self.active_mission.staged_files)} staged files:\n\t'
             staged_files = ((f"{file.origin_path.as_posix()} -> "
                             f"{file.target_path.relative_to(self.active_mission.path).as_posix()}")
-                                  for file in self.active_mission.staged_files)
+                                  for file in sorted(self.active_mission.staged_files,
+                                                     key=lambda x: x.target_path.name))
 
             output += '\n\t'.join(staged_files)
+        if len(self.active_dataset.staged_files) > 0:
+            output += f'{len(self.active_dataset.staged_files)} staged dataset files:\n\t'
+            output += '\n\t'.join(file.as_posix() for file in self.active_dataset.staged_files)
         return output
 
     def activate(self,

e4e_data_management/data.py

@@ -34,7 +34,7 @@ def __init__(self, path: Path, root: Optional[Path] = None):
         self.path = path
         if root is None:
             root = path.parent
-        self.__root = root
+        self.__root = root.resolve()
 
     def validate(self,
                  manifest: Dict[str, Dict[str, Union[str, int]]],
@@ -176,7 +176,7 @@ class Mission:
     """
     __MANIFEST_NAME = 'manifest.json'
     def __init__(self, path: Path, mission_metadata: Metadata) -> None:
-        self.path = path
+        self.path = path.resolve()
         self.metadata = mission_metadata
         self.committed_files: List[Path] = []
         self.staged_files: Set[StagedFile] = set()
@@ -242,7 +242,7 @@ def stage(self, paths: Iterable[Path], destination: Optional[Path] = None):
                     StagedFile(
                     origin_path=path.resolve(),
                     target_path=dst.joinpath(path.name).resolve(),
-                    hash=Manifest.compute_file_hash(path.absolute())
+                    hash=Manifest.compute_file_hash(path.resolve())
                     )
                 )
             elif path.is_dir():
@@ -296,7 +296,7 @@ class Dataset:
     VERSION = 1
 
     def __init__(self, root: Path, day_0: dt.date):
-        self.root = root
+        self.root = root.resolve()
         self.day_0: dt.date = day_0
         self.last_country: Optional[str] = None
         self.last_region: Optional[str] = None
@@ -481,7 +481,7 @@ def commit(self) -> List[Path]:
             new_files: List[Path] = []
             for file in added_files:
                 src = file
-                dest = self.root.joinpath(file.relative_to(root)).absolute()
+                dest = self.root.joinpath(file.relative_to(root)).resolve()
                 dest.parent.mkdir(parents=True, exist_ok=True)
                 copy2(src=src, dst=dest)
                 new_files.append(dest)

tests/conftest.py

@@ -27,7 +27,7 @@ def create_test_bare_app() -> MockAppFixture:
 
     """
     with TemporaryDirectory() as temp_dir:
-        root_dir = Path(temp_dir)
+        root_dir = Path(temp_dir).resolve()
         DataManager.config_dir = root_dir
         app = DataManager(
             app_config_dir=root_dir
@@ -62,7 +62,7 @@ def create_test_data() -> DataFixture:
     """
     random.seed(0)
     with TemporaryDirectory() as path:
-        data_dir = Path(path)
+        data_dir = Path(path).resolve()
         for file_idx in range(N_FILES):
             with open(data_dir.joinpath(f'{file_idx:04d}.bin'), 'wb') as handle:
                 # Python 3.8 doesn't have random.randbytes, so this is the bypass
@@ -81,7 +81,7 @@ def create_test_readme() -> Path:
         Path: README.md
     """
     with TemporaryDirectory() as path:
-        readme_path = Path(path).joinpath('readme.md')
+        readme_path = Path(path).joinpath('readme.md').resolve()
         with open(readme_path, 'w', encoding='ascii') as handle:
             handle.write('readme\n')
         yield readme_path

tests/test_cli.py

@@ -97,7 +97,7 @@ def test_add_files(single_mission: Tuple[Mock, DataManager, Path],
     data_dir, _, _ = test_data
 
     bin_files = list(data_dir.rglob('*.bin'))[:2]
-    args = split(f'e4edm add {bin_files[0].as_posix()} {bin_files[1].as_posix()}')
+    args = split(f'e4edm add "{bin_files[0].as_posix()}" "{bin_files[1].as_posix()}"')
     with patch('sys.argv', args):
         main()
         mock.add.assert_called_once_with(paths=bin_files, readme=False, destination=None)
@@ -141,7 +141,7 @@ def test_add_files_end(single_mission: Tuple[Mock, DataManager, Path],
 
     start_time = dt.datetime.now()
 
-    args = split(f'e4edm add {data_dir.as_posix()}/*.bin '
+    args = split(f'e4edm add "{data_dir.as_posix()}/*.bin" '
                  f'--end {start_time.isoformat()}')
     with patch('sys.argv', args):
         main()
@@ -158,7 +158,7 @@ def test_add_glob(single_mission: Tuple[Mock, DataManager, Path],
     mock, _, _ = single_mission
     data_dir, _, _ = test_data
 
-    args = split(f'e4edm add {data_dir.as_posix()}/*.bin')
+    args = split(f'e4edm add "{data_dir.as_posix()}/*.bin"')
     with patch('sys.argv', args):
         main()
         mock.add.assert_called_once_with(paths=list(data_dir.glob('*.bin')),
@@ -179,7 +179,7 @@ def test_add_multifile(single_mission: Tuple[Mock, DataManager, Path]):
     file2 = root_dir.joinpath('test2.txt')
     file2.touch()
 
-    args = split(f'e4edm add {file1.as_posix()} {file2.as_posix()}')
+    args = split(f'e4edm add "{file1.as_posix()}" "{file2.as_posix()}"')
     with patch('sys.argv', args):
         main()
         mock.add.assert_called_once_with(paths=[file1, file2], readme=False, destination=None)
@@ -230,7 +230,7 @@ def test_add_readme(single_mission: Tuple[Mock, DataManager, Path], test_readme:
     """
     mock, _, _ = single_mission
 
-    args = split(f'e4edm add --readme {test_readme.as_posix()}')
+    args = split(f'e4edm add --readme "{test_readme.as_posix()}"')
     with patch('sys.argv', args):
         main()
         mock.add.assert_called_once_with(paths=[test_readme], readme=True, destination=None)

tests/test_status.py

@@ -0,0 +1,28 @@
+'''Tests for the status output
+'''
+import re
+from pathlib import Path
+from typing import Tuple
+from unittest.mock import Mock
+
+from e4e_data_management.core import DataManager
+
+
+def test_readme_staging(single_mission: Tuple[Mock, DataManager, Path], test_readme: Path):
+    """Tests that a staged README file is displayed in the status output
+
+    Args:
+        single_mission (Tuple[Mock, DataManager, Path]): Single mission test app
+        test_readme (Path): Test Readme file
+    """
+    _, app, _ = single_mission
+
+    app.add([test_readme], readme=True)
+
+    status_output = app.status()
+
+    regex = r"readme\.md|readme\.docx"
+
+    matches = re.findall(regex, status_output, re.MULTILINE | re.IGNORECASE)
+
+    assert len(matches) != 0

tests/test_validator.py

@@ -17,7 +17,7 @@ def test_validation():
         NotImplementedError: Unsupported platform
     """
     with TemporaryDirectory() as temp_dir:
-        run_dir = Path(temp_dir)
+        run_dir = Path(temp_dir).resolve()
         for file_idx in range(N_FILES):
             with open(run_dir.joinpath(f'{file_idx:04d}.bin'), 'w', encoding='ascii') as handle:
                 for _ in range(N_BYTES):
@@ -37,7 +37,7 @@ def test_validation():
                 # Note: certUtil actually throws an error on empty string!  So we need to bypass...
                 if file.lstat().st_size != 0:
                     output = subprocess.check_output(
-                        ['certUtil', '-hashfile', file.absolute().as_posix(), 'SHA256'])
+                        ['certUtil', '-hashfile', file.resolve().as_posix(), 'SHA256'])
                     cksum = output.decode().splitlines()[1].strip()
                 else:
                     cksum = 'e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855'