Fix test problems

Author: TheByronHimes

src/ghga_connector/cli.py

@@ -16,12 +16,8 @@
 """CLI-specific wrappers around core functions."""
 
 import asyncio
-import logging
 import os
-import sys
-from functools import partial
 from pathlib import Path
-from types import TracebackType
 
 import typer
 
@@ -30,39 +26,7 @@
 from ghga_connector.constants import C4GH
 from ghga_connector.core import CLIMessageDisplay, async_client
 from ghga_connector.core.main import async_download, decrypt_file, upload_file
-
-
-def strtobool(value: str) -> bool:
-    """Inplace replacement for distutils.utils"""
-    return value.lower() in ("y", "yes", "on", "1", "true", "t")
-
-
-def exception_hook(
-    type_: BaseException,
-    value: BaseException,
-    traceback: TracebackType | None,
-):
-    """When debug mode is NOT enabled, gets called to perform final error handling
-    before program exits
-    """
-    message = (
-        "An error occurred. Rerun command"
-        + " with --debug at the end to see more information."
-    )
-
-    if value.args:
-        message += f"\n{value.args[0]}"
-
-    CLIMessageDisplay.failure(message)
-
-
-def modify_for_debug(debug: bool):
-    """Enable debug logging and configure exception printing if debug=True"""
-    if debug:
-        # enable debug logging
-        logging.basicConfig(level=logging.DEBUG)
-        sys.excepthook = partial(exception_hook)
-
+from ghga_connector.core.utils import modify_for_debug, strtobool
 
 cli = typer.Typer(no_args_is_help=True)
 

src/ghga_connector/core/downloading/batch_processing.py

@@ -220,3 +220,4 @@ async def manage_file_downloads(self, overwrite: bool) -> AsyncGenerator[FileInf
                 CLIMessageDisplay.success(
                     f"File with id '{file_info.file_id}' has been successfully downloaded."
                 )
+            staged_files.clear()

src/ghga_connector/core/utils.py

@@ -15,17 +15,53 @@
 
 """Various helper functions"""
 
+import logging
+import sys
+from functools import partial
 from pathlib import Path
+from types import TracebackType
 
 import crypt4gh.keys
 from ghga_service_commons.utils import crypt
 
 from ghga_connector import exceptions
-from ghga_connector.core.downloading.batch_processing import FileInfo
+from ghga_connector.core.downloading.structs import FileInfo
 from ghga_connector.core.message_display import CLIMessageDisplay
 from ghga_connector.core.structs import WorkPackageInformation
 
 
+def strtobool(value: str) -> bool:
+    """Inplace replacement for distutils.utils"""
+    return value.lower() in ("y", "yes", "on", "1", "true", "t")
+
+
+def exception_hook(
+    type_: BaseException,
+    value: BaseException,
+    traceback: TracebackType | None,
+):
+    """When debug mode is NOT enabled, gets called to perform final error handling
+    before program exits
+    """
+    message = (
+        "An error occurred. Rerun command"
+        + " with --debug at the end to see more information."
+    )
+
+    if value.args:
+        message += f"\n{value.args[0]}"
+
+    CLIMessageDisplay.failure(message)
+
+
+def modify_for_debug(debug: bool):
+    """Enable debug logging and configure exception printing if debug=True"""
+    if debug:
+        # enable debug logging
+        logging.basicConfig(level=logging.DEBUG)
+        sys.excepthook = partial(exception_hook)
+
+
 def get_work_package_information(my_private_key: bytes):
     """Fetch a work package id and work package token and decrypt the token"""
     # get work package access token and id from user input

tests/integration/test_cli.py

@@ -32,12 +32,12 @@
 from pytest_httpx import HTTPXMock, httpx_mock  # noqa: F401
 
 from ghga_connector import exceptions
-from ghga_connector.cli import async_download, modify_for_debug
 from ghga_connector.config import set_runtime_config
 from ghga_connector.constants import C4GH, DEFAULT_PART_SIZE
 from ghga_connector.core.client import async_client
 from ghga_connector.core.crypt import Crypt4GHEncryptor
-from ghga_connector.core.main import upload_file
+from ghga_connector.core.main import async_download, upload_file
+from ghga_connector.core.utils import modify_for_debug
 from tests.fixtures import state
 from tests.fixtures.config import get_test_config
 from tests.fixtures.mock_api.app import (
@@ -94,7 +94,7 @@ def apply_test_config():
     """Apply default test config"""
     with (
         patch("ghga_connector.config.CONFIG", get_test_config()),
-        patch("ghga_connector.cli.CONFIG", get_test_config()),
+        patch("ghga_connector.core.main.CONFIG", get_test_config()),
     ):
         yield
 
@@ -103,7 +103,7 @@ def apply_test_config():
 def apply_common_download_mocks(monkeypatch):
     """Monkeypatch download-specific functions and values"""
     monkeypatch.setattr(
-        "ghga_connector.cli.get_work_package_token", mock_work_package_token
+        "ghga_connector.core.utils.get_work_package_token", mock_work_package_token
     )
     monkeypatch.setattr(
         "ghga_connector.core.work_package._decrypt",