Impl. duplicates identification

lochness/config/__init__.py

@@ -1,52 +1,70 @@
+"""
+Module to read Lochness configuration file and keyring file.
+"""
+
+import getpass as gp
+import logging
 import os
+import string
+from typing import Any, Dict
+
+import cryptease as crypt
 import yaml
-import logging
 import yaml.reader
-import getpass as gp
-import cryptease as crypt
-import string
 
 logger = logging.getLogger(__name__)
 
 
-def load(f: 'location', archive_base=None):
-    '''load configuration file and keyring'''
-    logger.debug('loading configuration')
+def load(path: str, archive_base=None) -> Dict[str, Any]:
+    """
+    Load configuration file and keyring
+
+    Uses passphrase from environment variable NRG_KEYRING_PASS if available.
+    Otherwise, prompts user for passphrase.
+
+    Args:
+        path (str): path to configuration file (yaml)
+        archive_base (str): path to the root of the archive
 
-    with open(os.path.expanduser(f), 'rb') as fp:
-        Lochness = _read_config_file(fp)
+    Returns:
+        Dict[str, Any]: configuration dictionary
+    """
+    logger.debug("loading configuration")
+    Lochness = _read_config_file(path)
 
     if archive_base:
-        Lochness['phoenix_root'] = archive_base
-    if 'phoenix_root' not in Lochness:
-        raise ConfigError('need either --archive-base or '
-                          '\'phoenix_root\' in config file')
-    Lochness['phoenix_root'] = os.path.expanduser(Lochness['phoenix_root'])
-    Lochness['keyring_file'] = os.path.expanduser(Lochness['keyring_file'])
+        Lochness["phoenix_root"] = archive_base
+    if "phoenix_root" not in Lochness:
+        raise ConfigError(
+            "need either --archive-base or 'phoenix_root' in config file"
+        )
+    Lochness["phoenix_root"] = os.path.expanduser(Lochness["phoenix_root"])
+    Lochness["keyring_file"] = os.path.expanduser(Lochness["keyring_file"])
 
     # box file pattern strings from the config to string template
     # regardless of the selected study in the args
-    if 'box' in Lochness:
-        for _, study_dict in Lochness['box'].items():
-            for _, modality_values in study_dict['file_patterns'].items():
+    if "box" in Lochness:
+        for _, study_dict in Lochness["box"].items():
+            for _, modality_values in study_dict["file_patterns"].items():
                 for modality_dict in modality_values:
-                    modality_dict['pattern'] = \
-                        string.Template(modality_dict['pattern'])
+                    modality_dict["pattern"] = string.Template(modality_dict["pattern"])
 
-    with open(Lochness['keyring_file'], 'rb') as fp:
-        logger.info('reading keyring file {0}'.format(Lochness['keyring_file']))
-        if 'NRG_KEYRING_PASS' in os.environ:
-            load.passphrase = os.environ['NRG_KEYRING_PASS']
+    with open(Lochness["keyring_file"], "rb") as fp:
+        logger.info(f"reading keyring file {Lochness["keyring_file"]}")
+        if "NRG_KEYRING_PASS" in os.environ:
+            load.passphrase = os.environ["NRG_KEYRING_PASS"]
         if load.passphrase is None:
-            load.passphrase = gp.getpass('enter passphrase: ')
+            load.passphrase = gp.getpass("enter passphrase: ")
         key = crypt.key_from_file(fp, load.passphrase)
-        content = b''
+        content = b""
         for chunk in crypt.decrypt(fp, key):
             content += chunk
         try:
-            Lochness['keyring'] = yaml.load(content, Loader=yaml.FullLoader)
+            Lochness["keyring"] = yaml.load(content, Loader=yaml.FullLoader)
         except yaml.reader.ReaderError:
-            raise KeyringError('could not decrypt keyring {0} (wrong passphrase?)'.format(Lochness['keyring_file']))
+            raise KeyringError(
+                f"could not decrypt keyring {Lochness["keyring_file"]} (wrong passphrase?)"
+            )
 
     return Lochness
 
@@ -55,19 +73,24 @@ def load(f: 'location', archive_base=None):
 
 
 class KeyringError(Exception):
-    pass
+    """
+    Generic keyring error.
+    """
 
 
-def _read_config_file(fp):
-    '''helper to read lochness configuration file'''
-    try:
-        cfg = yaml.load(fp.read(), Loader=yaml.FullLoader)
-    except Exception as e:
-        raise ConfigError('failed to parse {0} with error: {1}'.format(fp.name, e))
-    return cfg
+def _read_config_file(path: str) -> Dict[str, Any]:
+    """helper to read lochness configuration file"""
 
-
-class ConfigError(Exception):
-    pass
+    expanded_path = os.path.expanduser(path)
+    with open(expanded_path, "rb") as fp:
+        try:
+            cfg = yaml.load(fp.read(), Loader=yaml.FullLoader)
+        except Exception as e:
+            raise ConfigError(f"failed to parse {expanded_path} with error: {e}")
+        return cfg
 
 
+class ConfigError(Exception):
+    """
+    Malformed configuration file.
+    """