feat: require passing the logger to the storage provider

Author: johanneskoester

README.md

@@ -68,6 +68,9 @@ class StorageProviderSettings(StorageProviderSettingsBase):
 # This class can be empty as the one below.
 # You can however use it to store global information or maintain e.g. a connection
 # pool.
+# Inside of the provider, you can use self.logger (a normal Python logger of type 
+# logging.Logger) to log any additional informations or
+# warnings.
 class StorageProvider(StorageProviderBase):
     # For compatibility with future changes, you should not overwrite the __init__
     # method. Instead, use __post_init__ to set additional attributes and initialize
@@ -129,6 +132,8 @@ class StorageProvider(StorageProviderBase):
 # storage (e.g. because it is read-only see
 # snakemake-storage-http for comparison), remove the corresponding base classes
 # from the list of inherited items.
+# Inside of the object, you can use self.provider to access the provider (e.g. for )
+# self.provider.logger, see above, or self.provider.settings).
 class StorageObject(
     StorageObjectRead,
     StorageObjectWrite,

snakemake_interface_storage_plugins/storage_provider.py

@@ -8,6 +8,7 @@
 from dataclasses import dataclass
 from enum import Enum
 from fractions import Fraction
+from logging import Logger
 from pathlib import Path
 import sys
 from abc import ABC, abstractmethod
@@ -57,11 +58,13 @@ class StorageProviderBase(ABC):
     def __init__(
         self,
         local_prefix: Path,
+        logger: Logger,
         settings: Optional[StorageProviderSettingsBase] = None,
         keep_local=False,
         retrieve=True,
         is_default=False,
     ):
+        self.logger: Logger = logger
         try:
             local_prefix.mkdir(parents=True, exist_ok=True)
         except OSError as e:

snakemake_interface_storage_plugins/tests.py

@@ -5,6 +5,7 @@
 
 from abc import ABC, abstractmethod
 import asyncio
+import logging
 from pathlib import Path
 import shutil
 import sys
@@ -20,6 +21,9 @@
 from snakemake.io import IOCache
 
 
+logger = logging.getLogger(__name__)
+
+
 class TestStorageBase(ABC):
     __test__ = False
     retrieve_only = False
@@ -129,6 +133,7 @@ def test_query_validation(self, tmp_path):
 
     def _get_provider(self, tmp_path):
         return self.get_storage_provider_cls()(
+            logger=logger,
             local_prefix=Path(tmp_path) / "local_prefix",
             settings=self.get_storage_provider_settings(),
         )