Refactor config2

alphadia/search_step.py

@@ -32,7 +32,6 @@ def __init__(
         config: dict | Config | None = None,
         cli_config: dict | None = None,
         extra_config: dict | None = None,
-        config_base_path: str | None = None,
     ) -> None:
         """Highest level class to plan a DIA search step.
 
@@ -46,24 +45,22 @@ def __init__(
             output folder to save the results
 
         config : dict, optional
-            values to update the default config. Overrides values in `default.yaml` and `config_base_path`.
+            values to update the default config. Overrides values in `default.yaml`.
 
         cli_config : dict, optional
             additional config values (parameters from the command line). Overrides values in `config`.
 
         extra_config : dict, optional
             additional config values (parameters to orchestrate multistep searches). Overrides values in `config` and `cli_config`.
 
-        config_base_path : str, optional
-            absolute path to yaml file containing additional config values. Overrides values in `default.yaml`.
         """
 
         self.output_folder = output_folder
         os.makedirs(output_folder, exist_ok=True)
         reporting.init_logging(self.output_folder)
 
         self._config = self._init_config(
-            config, cli_config, extra_config, output_folder, config_base_path
+            config, cli_config, extra_config, output_folder
         )
         logger.setLevel(logging.getLevelName(self._config["general"]["log_level"]))
 
@@ -86,7 +83,6 @@ def _init_config(
         cli_config: dict | None,
         extra_config: dict | None,
         output_folder: str,
-        config_base_path: str | None,
     ) -> Config:
         """Initialize the config with default values and update with user defined values."""
 
@@ -98,18 +94,12 @@ def _init_config(
         config.from_yaml(default_config_path)
 
         config_updates = []
-        if config_base_path is not None:
-            logger.info(f"loading additional config from {config_base_path}")
-            user_config_from_file = Config(USER_DEFINED)
-            user_config_from_file.from_yaml(default_config_path)
-            config_updates.append(user_config_from_file)
 
         if user_config is not None:
             logger.info("loading additional config provided via CLI")
             # load update config from dict
             if isinstance(user_config, dict):
-                user_config_update = Config(USER_DEFINED)
-                user_config_update.from_dict(user_config)
+                user_config_update = Config(user_config, name=USER_DEFINED)
                 config_updates.append(user_config_update)
             elif isinstance(user_config, Config):
                 config_updates.append(user_config)
@@ -120,14 +110,12 @@ def _init_config(
 
         if cli_config is not None:
             logger.info("loading additional config provided via CLI parameters")
-            cli_config_update = Config(USER_DEFINED_CLI_PARAM)
-            cli_config_update.from_dict(cli_config)
+            cli_config_update = Config(cli_config, name=USER_DEFINED_CLI_PARAM)
             config_updates.append(cli_config_update)
 
         # this needs to be last
         if extra_config is not None:
-            extra_config_update = Config(MULTISTEP_SEARCH)
-            extra_config_update.from_dict(extra_config)
+            extra_config_update = Config(extra_config, name=MULTISTEP_SEARCH)
             # need to overwrite user-defined output folder here to have correct value in config dump
             extra_config[ConfigKeys.OUTPUT_DIRECTORY] = output_folder
             config_updates.append(extra_config_update)
@@ -304,12 +292,10 @@ def run(
                 workflow = self._process_raw_file(dia_path, raw_name, speclib)
                 workflow_folder_list.append(workflow.path)
 
-            except CustomError as e:
-                _log_exception_event(e, raw_name, workflow)
-                continue
-
             except Exception as e:
                 _log_exception_event(e, raw_name, workflow)
+                if isinstance(e, CustomError):
+                    continue
                 raise e
 
             finally:

alphadia/workflow/config.py

@@ -9,9 +9,8 @@
 
 import json
 import logging
-from collections import defaultdict
+from collections import UserDict, defaultdict
 from copy import deepcopy
-from typing import Any
 
 import yaml
 
@@ -25,54 +24,37 @@
 MULTISTEP_SEARCH = "multistep search"
 
 
-class Config:
-    """Class holding a configuration.
+class Config(UserDict):
+    """Dict-like config class that can read from and write to yaml and json files and allows updating with other config objects."""
 
-    Can read from and write to yaml and json files.
-    Can be used to update the config with other config objects, and print the config in a tree structure.
-    """
-
-    def __init__(self, name: str = "default") -> None:
+    def __init__(self, data: dict = None, name: str = DEFAULT) -> None:
+        # super class deliberately not called as this calls "update" (which we overwrite)
+        self.data = (
+            {**data} if data is not None else {}
+        )  # this needs to be called 'data' as we inherit from UserDict
         self.name = name
-        self.config = {}
-        self.translated_config = {}
 
     def from_yaml(self, path: str) -> None:
         with open(path) as f:
-            self.config = yaml.safe_load(f)
+            self.data = yaml.safe_load(f)
 
     def from_json(self, path: str) -> None:
         with open(path) as f:
-            self.config = json.load(f)
+            self.data = json.load(f)
 
     def to_yaml(self, path: str) -> None:
         with open(path, "w") as f:
-            yaml.dump(self.config, f, sort_keys=False)
+            yaml.dump(self.data, f, sort_keys=False)
 
     def to_json(self, path: str) -> None:
         with open(path, "w") as f:
-            json.dump(self.config, f)
-
-    def from_dict(self, config: dict[str, Any]) -> None:
-        self.config = config
-
-    def to_dict(self) -> dict[str, Any]:
-        return self.config
-
-    def get(self, key: str, default: Any = None) -> Any:
-        return self.config.get(key, default)
+            json.dump(self.data, f)
 
-    def __getitem__(self, key: str) -> Any:
-        return self.config[key]
+    def __setitem__(self, key, item):
+        raise NotImplementedError("Use update() to update the config.")
 
-    def __setitem__(self, key: str, value: Any) -> None:
-        self.config[key] = value
-
-    def __contains__(self, key: str) -> bool:
-        return key in self.config
-
-    def __repr__(self) -> str:
-        return str(self.config)
+    def __delitem__(self, key):
+        raise NotImplementedError("Use update() to update the config.")
 
     def update(self, configs: list["Config"], do_print: bool = False):
         """
@@ -92,29 +74,27 @@ def update(self, configs: list["Config"], do_print: bool = False):
         do_print : bool, optional
             Whether to print the modified config. Default is False.
         """
-
-        # we assume that self.config holds the default config
-        default_config = deepcopy(self.config)
+        # we assume that self.data holds the default config
+        default_config = deepcopy(self.data)
 
         def _recursive_defaultdict():
             """Allow initialization of an infinitely nested dictionary to be able to map arbitrary structures."""
             return defaultdict(_recursive_defaultdict)
 
         tracking_dict = defaultdict(_recursive_defaultdict)
 
-        current_config = deepcopy(self.config)
-
+        current_config = deepcopy(self.data)
         for config in configs:
             logger.info(f"Updating config with '{config.name}'")
 
             _update(
                 current_config,
-                config.to_dict(),
+                config.data,
                 tracking_dict,
                 config.name,
             )
 
-        self.config = current_config
+        self.data = current_config
 
         if do_print:
             try:

tests/e2e_tests/prepare_test_data.py

@@ -26,9 +26,9 @@ class YamlKeys:
     TEST_CASES = "test_cases"
     NAME = "name"
     CONFIG = "config"
-    LIBRARY = "library"
-    FASTA = "fasta"
-    RAW_DATA = "raw_data"
+    LIBRARY = "library_path"
+    FASTA = "fasta_paths"
+    RAW_DATA = "raw_paths"
     SOURCE_URL = "source_url"