Fix up loading/storing configs + unit tests

src/auto_archiver/core/config.py

@@ -6,12 +6,17 @@ flexible setup in various environments.
 """
 
 import argparse
-import yaml
+from ruamel.yaml import YAML, CommentedMap
+from ruamel.yaml.comments import CommentedMap
+
 from dataclasses import dataclass, field
 from collections import OrderedDict
-
+from collections.abc import Iterable
+from copy import deepcopy
 from .loader import MODULE_TYPES
 
+from typing import Any, List
+
 #     configurable_parents = [
 #         Feeder,
 #         Enricher,
@@ -50,21 +55,16 @@ from .loader import MODULE_TYPES
         #     parser.add_argument('--config', action='store', dest='config', help='the filename of the YAML configuration file (defaults to \'config.yaml\')', default='orchestration.yaml')
         #     parser.add_argument('--version', action='version', version=__version__)
 
-EMPTY_CONFIG = {
+EMPTY_CONFIG = CommentedMap(**{
     "steps": dict((f"{module_type}s", []) for module_type in MODULE_TYPES)
-}
+})
-class LoadFromFile (argparse.Action):
-    def __call__ (self, parser, namespace, values, option_string = None):
-        with values as f:
-            # parse arguments in the file and store them in the target namespace
-            parser.parse_args(f.read().split(), namespace)
 
-def to_dot_notation(yaml_conf: str) -> argparse.ArgumentParser:
+def to_dot_notation(yaml_conf: CommentedMap | dict) -> argparse.ArgumentParser:
     dotdict = {}
 
     def process_subdict(subdict, prefix=""):
         for key, value in subdict.items():
-            if type(value) == dict:
+            if is_dict_type(value):
                 process_subdict(value, f"{prefix}{key}.")
             else:
                 dotdict[f"{prefix}{key}"] = value
@@ -72,31 +72,64 @@ def to_dot_notation(yaml_conf: str) -> argparse.ArgumentParser:
     process_subdict(yaml_conf)
     return dotdict
 
-def merge_dicts(dotdict, yaml_dict):
+def from_dot_notation(dotdict: dict) -> dict:
-    def process_subdict(subdict, prefix=""):
+    normal_dict = {}
-        for key, value in subdict.items():
+
-            if "." in key:
+    def add_part(key, value, current_dict):
-                keys = key.split(".")
+        if "." in key:
-                subdict = yaml_dict
+            key_parts = key.split(".")
-                for k in keys[:-1]:
+            current_dict.setdefault(key_parts[0], {})
-                    subdict = subdict.setdefault(k, {})
+            add_part(".".join(key_parts[1:]), value, current_dict[key_parts[0]])
-                subdict[keys[-1]] = value
+        else:
-            else:
+            current_dict[key] = value
-                yaml_dict[key] = value
+
+    for key, value in dotdict.items():
+        add_part(key, value, normal_dict)
+
+    return normal_dict
+
+
+def is_list_type(value):
+    return isinstance(value, list) or isinstance(value, tuple) or isinstance(value, set)
+
+def is_dict_type(value):
+    return isinstance(value, dict) or isinstance(value, CommentedMap)
+
+def merge_dicts(dotdict: dict, yaml_dict: CommentedMap) -> CommentedMap:
+    yaml_dict: CommentedMap = deepcopy(yaml_dict)
+
+    # first deal with lists, since 'update' replaces lists from a in b, but we want to extend
+    def update_dict(subdict, yaml_subdict):
+        for key, value in yaml_subdict.items():
+            if not subdict.get(key):
+                continue
+
+            if is_dict_type(value):
+                update_dict(subdict[key], value)
+            elif is_list_type(value):
+                yaml_subdict[key].extend(s for s in subdict[key] if s not in yaml_subdict[key])
+            else:
+                yaml_subdict[key] = subdict[key]
+
+    update_dict(from_dot_notation(dotdict), yaml_dict)
 
-    process_subdict(dotdict)
     return yaml_dict
 
-def read_yaml(yaml_filename: str) -> dict:
+yaml = YAML()
 
+def read_yaml(yaml_filename: str) -> CommentedMap:
+    config = None
     try:
         with open(yaml_filename, "r", encoding="utf-8") as inf:
-            config = yaml.safe_load(inf)
+            config = yaml.load(inf)
     except FileNotFoundError:
+        pass
+
+    if not config:
         config = EMPTY_CONFIG
     
     return config
 
-def store_yaml(config: dict, yaml_filename: str):
+def store_yaml(config: CommentedMap, yaml_filename: str):
     with open(yaml_filename, "w", encoding="utf-8") as outf:
-        yaml.dump(config, outf, default_flow_style=False)
+        yaml.dump(config, outf)

src/auto_archiver/core/loader.py

@@ -91,7 +91,11 @@ def load_module(module: str) -> object: # TODO: change return type to Step
 
     logger.info(f"Loading module '{module.display_name}'...")
     loaded_module = __import__(qualname)
-    _LOADED_MODULES[module.name] = getattr(sys.modules[qualname], module.entry_point)()
+    instance = getattr(sys.modules[qualname], module.entry_point)()
+    if not getattr(instance, 'name', None):
+        instance.name = module.name
+
+    _LOADED_MODULES[module.name] = instance
     return _LOADED_MODULES[module.name]
 
 
@@ -109,7 +113,7 @@ def load_manifest(module_path):
 def get_module(module_name):
     # get a module by name
     try:
-        return available_modules(limit_to_modules=[module_name], with_manifest=True, suppress_warnings=True)[0]
+        return available_modules(limit_to_modules=[module_name], with_manifest=True)[0]
     except IndexError:
         return None
 
@@ -149,6 +153,6 @@ def available_modules(with_manifest: bool=False, limit_to_modules: List[str]= []
     if not suppress_warnings:
         for module in limit_to_modules:
             if not any(module == m.name for m in all_modules):
-                logger.warning(f"Module '{module}' not found in available modules. Are you sure it's installed?")
+                logger.warning(f"Module '{module}' not found. Are you sure it's installed?")
 
     return all_modules

src/auto_archiver/core/orchestrator.py

@@ -10,7 +10,7 @@ from urllib.parse import urlparse
 from ipaddress import ip_address
 import argparse
 import os
-from os.path import join, dirname
+import sys
 
 from rich_argparse import RichHelpFormatter
 
@@ -27,6 +27,14 @@ from loguru import logger
 
 DEFAULT_CONFIG_FILE = "orchestration.yaml"
 
+class UniqueAppendAction(argparse.Action):
+    def __call__(self, parser, namespace, values, option_string=None):
+        if not hasattr(namespace, self.dest):
+            setattr(namespace, self.dest, [])
+        for value in values:
+            if value not in getattr(namespace, self.dest):
+                getattr(namespace, self.dest).append(value)
+
 class ArchivingOrchestrator:
 
     # def __init__(self, config: Config) -> None:
@@ -59,20 +67,22 @@ class ArchivingOrchestrator:
         parser.add_argument('--mode', action='store', dest='mode', type=str, choices=['simple', 'full'], help='the mode to run the archiver in', default='simple')
         # override the default 'help' so we can inject all the configs and show those
         parser.add_argument('-h', '--help', action='store_true', dest='help', help='show this help message and exit')
-        parser.add_argument('-s', '--store', action='store_true', dest='store', help='Store the created config in the config file')
+        parser.add_argument('-s', '--store', dest='store', default=True, help='Store the created config in the config file', action=argparse.BooleanOptionalAction)
+
         self.basic_parser = parser
 
     def setup_complete_parser(self, basic_config: dict, yaml_config: dict, unused_args: list[str]) -> None:
         parser = argparse.ArgumentParser(
-            parents = [self.basic_parser],
             add_help=False,
         )
-        self.add_steps_args(parser)
+        self.add_additional_args(parser)
 
         # check what mode we're in
         # if we have a config file, use that to decide which modules to load
         # if simple, we'll load just the modules that has requires_setup = False
         # if full, we'll load all modules
+        # TODO: BUG** - basic_config won't have steps in it, since these args aren't added to 'basic_parser'
+        # but should we add them? Or should we just add them to the 'complete' parser?
         if yaml_config != EMPTY_CONFIG:
             # only load the modules enabled in config
             # TODO: if some steps are empty (e.g. 'feeders' is empty), should we default to the 'simple' ones? Or only if they are ALL empty?
@@ -85,7 +95,7 @@ class ArchivingOrchestrator:
                 if modules := getattr(basic_config, f"{module_type}s", []):
                     enabled_modules.extend(modules)
 
-            self.add_module_args(available_modules(with_manifest=True, limit_to_modules=set(enabled_modules)), parser)
+            self.add_module_args(available_modules(with_manifest=True, limit_to_modules=set(enabled_modules), suppress_warnings=True), parser)
         elif basic_config.mode == 'simple':
             simple_modules = [module for module in available_modules(with_manifest=True) if not module.requires_setup]
             self.add_module_args(simple_modules, parser)
@@ -97,36 +107,45 @@ class ArchivingOrchestrator:
             # load all modules, they're not using the 'simple' mode
             self.add_module_args(available_modules(with_manifest=True), parser)
         
-
-        breakpoint()
         parser.set_defaults(**to_dot_notation(yaml_config))
 
+        breakpoint()
         # reload the parser with the new arguments, now that we have them
         parsed, unknown = parser.parse_known_args(unused_args)
+
+        # merge the new config with the old one
+        self.config = merge_dicts(vars(parsed), yaml_config)
+        # clean out args from the base_parser that we don't want in the config
+        for key in vars(basic_config):
+            self.config.pop(key, None)
+
+        # setup the logging
+        self.setup_logging()
+
         if unknown:
             logger.warning(f"Ignoring unknown/unused arguments: {unknown}\nPerhaps you don't have this module enabled?")
 
-        # merge the new config with the old one
+        if (self.config != yaml_config and basic_config.store) or not os.path.isfile(basic_config.config_file):
-        merged_yaml_config = merge_dicts(vars(parsed), yaml_config)
-
-        if (merged_yaml_config != yaml_config and basic_config.store) or not os.path.isfile(basic_config.config_file):
             logger.info(f"Storing configuration file to {basic_config.config_file}")
-            store_yaml(yaml_config, basic_config.config_file)
+            store_yaml(self.config, basic_config.config_file)
-        
-        self.config = merged_yaml_config
         
         return self.config
     
-    def add_steps_args(self, parser: argparse.ArgumentParser = None):
+    def add_additional_args(self, parser: argparse.ArgumentParser = None):
         if not parser:
             parser = self.parser
 
-        parser.add_argument('--feeders', action='store', dest='steps.feeders', nargs='+', help='the feeders to use')
+        parser.add_argument('--feeders', dest='steps.feeders', nargs='+', help='the feeders to use', action=UniqueAppendAction)
-        parser.add_argument('--enrichers', action='store', dest='steps.enrichers',  nargs='+', help='the enrichers to use')
+        parser.add_argument('--enrichers', dest='steps.enrichers',  nargs='+', help='the enrichers to use', action=UniqueAppendAction)
-        parser.add_argument('--extractors', action='store', dest='steps.extractors', nargs='+', help='the extractors to use')
+        parser.add_argument('--extractors', dest='steps.extractors', nargs='+', help='the extractors to use', action=UniqueAppendAction)
-        parser.add_argument('--databases', action='store', dest='steps.databases', nargs='+', help='the databases to use')
+        parser.add_argument('--databases', dest='steps.databases', nargs='+', help='the databases to use', action=UniqueAppendAction)
-        parser.add_argument('--storages', action='store', dest='steps.storages', nargs='+', help='the storages to use')
+        parser.add_argument('--storages', dest='steps.storages', nargs='+', help='the storages to use', action=UniqueAppendAction)
-        parser.add_argument('--formatters', action='store', dest='steps.formatters', nargs='+', help='the formatter to use')
+        parser.add_argument('--formatters', dest='steps.formatters', nargs='+', help='the formatter to use', action=UniqueAppendAction)
+
+        # logging arguments
+        parser.add_argument('--logging.level', action='store', dest='logging.level', choices=['INFO', 'DEBUG', 'ERROR', 'WARNING'], help='the logging level to use', default='INFO')
+        parser.add_argument('--logging.file', action='store', dest='logging.file', help='the logging file to write to', default=None)
+        parser.add_argument('--logging.rotation', action='store', dest='logging.rotation', help='the logging rotation to use', default=None)
 
     def add_module_args(self, modules: list[Module] = None, parser: argparse.ArgumentParser = None):
 
@@ -152,20 +171,29 @@ class ArchivingOrchestrator:
         # for the help message, we want to load *all* possible modules and show the help
             # add configs as arg parser arguments
         
-        self.add_steps_args(self.basic_parser)
+        self.add_additional_args(self.basic_parser)
         self.add_module_args(parser=self.basic_parser)
 
         self.basic_parser.print_help()
         exit()
     
+    def setup_logging(self):
+        # setup loguru logging
+        logger.remove() # remove the default logger
+
+        logging_config = self.config['logging']
+        logger.add(sys.stderr, level=logging_config['level'])
+        if log_file := logging_config['file']:
+            logger.add(log_file, rotation=logging_config['logging.rotation'])
+
+        
     def install_modules(self):
         """
         Swaps out the previous 'strings' in the config with the actual modules
         """
         
+        invalid_modules = []
         for module_type in MODULE_TYPES:
-            if module_type == 'enricher':
-                breakpoint()
             step_items = []
             modules_to_load = self.config['steps'][f"{module_type}s"]
 
@@ -179,7 +207,12 @@ class ArchivingOrchestrator:
                     exit()
 
             for i, module in enumerate(modules_to_load):
+                if module in invalid_modules:
+                    continue
                 loaded_module = load_module(module)
+                if not loaded_module:
+                    invalid_modules.append(module)
+                    continue
                 if loaded_module:
                     step_items.append(loaded_module)
             check_steps_ok()
@@ -228,7 +261,6 @@ class ArchivingOrchestrator:
     def cleanup(self)->None:
         logger.info("Cleaning up")
         for e in self.config['steps']['extractors']:
-            breakpoint()
             e.cleanup()
 
     def feed(self) -> Generator[Metadata]:

src/auto_archiver/core/step.py

@@ -7,5 +7,5 @@ by handling user configuration, validating the steps properties, and implementin
 from __future__ import annotations
 
 class Step:
-    # TODO: try and get this name from the manifest, so we don't have to set it twice
+    # Nothing to see here :)
-    name: str
+    pass

tests/test_config.py

@@ -0,0 +1,99 @@
+import pytest
+from auto_archiver.core import config
+from ruamel.yaml.scanner import ScannerError
+from ruamel.yaml.comments import CommentedMap
+
+def test_return_default_config_for_nonexistent_file():
+    assert config.read_yaml("nonexistent_file.yaml") == config.EMPTY_CONFIG
+
+def test_return_default_config_for_empty_file(tmp_path):
+    empty_file = tmp_path / "empty_file.yaml"
+    empty_file.write_text("")
+    assert config.read_yaml(empty_file) == config.EMPTY_CONFIG
+
+def test_raise_error_on_invalid_yaml(tmp_path):
+    invalid_yaml = tmp_path / "invalid_yaml.yaml"
+    invalid_yaml.write_text("key: \"value_without_end_quote")
+    # make sure it raises ScannerError
+    with pytest.raises(ScannerError):
+        config.read_yaml(invalid_yaml)
+
+def test_write_yaml(tmp_path):
+    yaml_file = tmp_path / "write_yaml.yaml"
+    config.store_yaml(config.EMPTY_CONFIG, yaml_file.as_posix())
+    assert "steps:\n" in yaml_file.read_text()
+
+def test_round_trip_comments(tmp_path):
+    yaml_file = tmp_path / "round_trip_comments.yaml"
+
+    with open(yaml_file, "w") as f:
+        f.write("generic_extractor:\n  facebook_cookie: abc # end of line comment\n  subtitles: true\n  # comments: false\n  # livestreams: false\n  list_type:\n    - value1\n    - value2")
+
+    loaded = config.read_yaml(yaml_file)
+    # check the comments are preserved
+    assert loaded['generic_extractor']['facebook_cookie'] == "abc"
+    assert loaded['generic_extractor'].ca.items['facebook_cookie'][2].value == "# end of line comment\n"
+
+    # add some more items to my_settings
+    loaded['generic_extractor']['list_type'].append("bellingcat")
+    config.store_yaml(loaded, yaml_file.as_posix())
+
+    assert "# comments: false" in yaml_file.read_text()
+    assert "facebook_cookie: abc # end of line comment" in yaml_file.read_text()
+    assert "abc # end of line comment" in yaml_file.read_text()
+    assert "- value2\n  - bellingcat" in yaml_file.read_text()
+
+def test_merge_dicts():
+    yaml_dict = config.EMPTY_CONFIG
+    yaml_dict['settings'] = CommentedMap(**{
+            "key1": ["a"],
+            "key2": "old_value",
+            "key3": ["a", "b", "c"],
+        })
+
+    dotdict = {
+        "settings.key1": ["b", "c"],
+        "settings.key2": "new_value",
+        "settings.key3": ["b", "c", "d"],
+    }
+    merged = config.merge_dicts(dotdict, yaml_dict)
+    assert merged["settings"]["key1"] == ["a", "b", "c"]
+    assert merged["settings"]["key2"] == "new_value"
+    assert merged["settings"]["key3"] == ["a", "b", "c", "d"]
+
+
+def test_check_types():
+    assert config.is_list_type([]) == True
+    assert config.is_list_type(()) == True
+    assert config.is_list_type(set()) == True
+    assert config.is_list_type({}) == False
+    assert config.is_list_type("") == False
+    assert config.is_dict_type({}) == True
+    assert config.is_dict_type(CommentedMap()) == True
+    assert config.is_dict_type([]) == False
+    assert config.is_dict_type("") == False
+
+def test_from_dot_notation():
+    dotdict = {
+        "settings.key1": ["a", "b", "c"],
+        "settings.key2": "new_value",
+        "settings.key3.key4": "value",
+    }
+    normal_dict = config.from_dot_notation(dotdict)
+    assert normal_dict["settings"]["key1"] == ["a", "b", "c"]
+    assert normal_dict["settings"]["key2"] == "new_value"
+    assert normal_dict["settings"]["key3"]["key4"] == "value"
+
+def test_to_dot_notation():
+    yaml_dict = config.EMPTY_CONFIG
+    yaml_dict['settings'] = {
+        "key1": ["a", "b", "c"],
+        "key2": "new_value",
+        "key3": {
+            "key4": "value",
+        }
+    }
+    dotdict = config.to_dot_notation(yaml_dict)
+    assert dotdict["settings.key1"] == ["a", "b", "c"]
+    assert dotdict["settings.key2"] == "new_value"
+    assert dotdict["settings.key3.key4"] == "value"