from pathlib import Path import pytest from galaxy.config import BaseAppConfiguration from galaxy.config.schema import AppSchema MOCK_DEPRECATED_DIRS = { "my_config_dir": "old-config", "my_data_dir": "old-database", } # Mock properties loaded from schema (all options represent paths) MOCK_SCHEMA = { "my_config_dir": { "type": "str", "default": "my-config", }, "my_data_dir": { "type": "str", "default": "my-data", }, "path1": { "type": "str", "default": "my-config-files", "path_resolves_to": "my_config_dir", }, "path2": { "type": "str", "default": "my-data-files", "path_resolves_to": "my_data_dir", }, "path3": { "type": "str", "default": "my-other-files", }, "path4": { "type": "str", "default": "conf1, conf2, conf3", "path_resolves_to": "my_config_dir", }, } def get_schema(app_mapping): return {"mapping": {"_": {"mapping": app_mapping}}} @pytest.fixture def mock_init(monkeypatch): monkeypatch.setattr(BaseAppConfiguration, "_load_schema", lambda a: AppSchema(Path("no path"), "_")) monkeypatch.setattr(AppSchema, "_read_schema", lambda a, b: get_schema(MOCK_SCHEMA)) monkeypatch.setattr(BaseAppConfiguration, "deprecated_dirs", MOCK_DEPRECATED_DIRS) monkeypatch.setattr(BaseAppConfiguration, "listify_options", {"path4"}) def test_mock_schema_is_loaded(mock_init): # Check that mock is loaded as expected config = BaseAppConfiguration() assert len(config._raw_config) == 6 assert config._raw_config["my_config_dir"] == "my-config" assert config._raw_config["my_data_dir"] == "my-data" assert config._raw_config["path1"] == "my-config-files" assert config._raw_config["path2"] == "my-data-files" assert config._raw_config["path3"] == "my-other-files" assert config._raw_config["path4"] == "conf1, conf2, conf3" def test_no_kwargs(mock_init): # Expected: use default from schema, then resolve config = BaseAppConfiguration() assert config.path1 == "my-config/my-config-files" # resolved assert config.path2 == "my-data/my-data-files" # resolved assert config.path3 == "my-other-files" # no change assert config.path4 == [ "my-config/conf3" ] # last value resolved and listified; others dropped as files do not exist def test_kwargs_relative_path(mock_init): # Expected: use value from kwargs, then resolve new_path1 = "foo1/bar" new_path2 = "foo2/bar" config = BaseAppConfiguration(path1=new_path1, path2=new_path2) assert config.path1 == "my-config/" + new_path1 # resolved assert config.path2 == "my-data/" + new_path2 # resolved assert config.path3 == "my-other-files" # no change def test_kwargs_absolute_path(mock_init): # Expected: use value from kwargs, do NOT resolve new_path1 = "/foo1/bar" new_path2 = "/foo2/bar" config = BaseAppConfiguration(path1=new_path1, path2=new_path2) assert config.path1 == new_path1 # NOT resolved assert config.path2 == new_path2 # NOT resolved assert config.path3 == "my-other-files" # no change def test_kwargs_relative_path_old_prefix(mock_init): # Expect: use value from kwargs, strip old prefix, then resolve new_path1 = "old-config/foo1/bar" new_path2 = "old-database/foo2/bar" config = BaseAppConfiguration(path1=new_path1, path2=new_path2) assert config.path1 == "my-config/foo1/bar" # stripped of old prefix, resolved assert config.path2 == "my-data/foo2/bar" # stripped of old prefix, resolved assert config.path3 == "my-other-files" # no change def test_kwargs_relative_path_old_prefix_csv_value(mock_init): # Expect: use value from kwargs, split at commas, then for each path strip # spaces, strip old prefix if needed, and resolve if needed config = BaseAppConfiguration(path4="old-config/foo/file1 , /foo1/bar, foo/file3") assert config.path4 == ["my-config/foo/file1", "/foo1/bar", "my-config/foo/file3"] def test_kwargs_relative_path_old_prefix_for_other_option(mock_init): # Expect: use value from kwargs, do NOT strip old prefix, then resolve # Reason: deprecated dirs are option-specific: we don't want to strip 'old-config' # (deprecated for the config_dir option) if it's used for another option new_path1 = "old-database/foo1/bar" new_path2 = "old-config/foo2/bar" config = BaseAppConfiguration(path1=new_path1, path2=new_path2) assert config.path1 == "my-config/" + new_path1 # resolved assert config.path2 == "my-data/" + new_path2 # resolved assert config.path3 == "my-other-files" # no change def test_kwargs_relative_path_old_prefix_empty_after_strip(mock_init): # Expect: use value from kwargs, strip old prefix, then resolve new_path1 = "old-config/foo" config = BaseAppConfiguration(path1=new_path1) assert config.path1 == "my-config/foo" # stripped of old prefix, then resolved assert config.path2 == "my-data/my-data-files" # stripped of old prefix, then resolved assert config.path3 == "my-other-files" # no change def test_kwargs_set_to_null(mock_init): # Expected: allow overriding with null # This is not a common scenario, but it does happen: one example is # `job_config` set to `None` when testing config = BaseAppConfiguration(path1=None) assert config.path1 is None assert config.path2 == "my-data/my-data-files" # resolved assert config.path3 == "my-other-files" # no change def test_add_sample_file(mock_init, monkeypatch): # Expected: sample file appended to list of defaults: # - resolved w.r.t sample-dir (_in_sample_dir mocked) # - has ".sample" suffix # Last value (sample file) resolved and listified; others dropped as files do not exist monkeypatch.setattr(BaseAppConfiguration, "add_sample_file_to_defaults", {"path1", "path4"}) monkeypatch.setattr(BaseAppConfiguration, "_in_sample_dir", lambda a, path: f"/sample-dir/{path}") config = BaseAppConfiguration() assert config._raw_config["path1"] == "my-config-files" assert config.path1 == "/sample-dir/my-config-files.sample" assert config._raw_config["path4"] == "conf1, conf2, conf3" assert config.path4 == ["/sample-dir/conf3.sample"] def test_select_one_path_from_list(mock_init, monkeypatch): # Expected: files do not exist, so use last file in list (would be sample file); value is not a list monkeypatch.setattr(BaseAppConfiguration, "add_sample_file_to_defaults", {"path1"}) monkeypatch.setattr(BaseAppConfiguration, "_in_sample_dir", lambda a, path: f"/sample-dir/{path}") config = BaseAppConfiguration() assert config._raw_config["path1"] == "my-config-files" assert config.path1 == "/sample-dir/my-config-files.sample" def test_select_one_path_from_list_all_files_exist(mock_init, monkeypatch): # Expected: all files exist, so use first file in list; value is not a list monkeypatch.setattr(BaseAppConfiguration, "add_sample_file_to_defaults", {"path1"}) monkeypatch.setattr(BaseAppConfiguration, "_path_exists", lambda a, b: True) config = BaseAppConfiguration() assert config._raw_config["path1"] == "my-config-files" assert config.path1 == "my-config/my-config-files" def test_no_kwargs_listify(mock_init, monkeypatch): # Expected: last value resolved and listified; others dropped as files do not exist config = BaseAppConfiguration() assert config._raw_config["path4"] == "conf1, conf2, conf3" assert config.path4 == ["my-config/conf3"] def test_no_kwargs_listify_all_files_exist(mock_init, monkeypatch): # Expected: each value resolved and listified (mock: all files exist) monkeypatch.setattr(BaseAppConfiguration, "_path_exists", lambda a, b: True) config = BaseAppConfiguration() assert config._raw_config["path4"] == "conf1, conf2, conf3" assert config.path4 == ["my-config/conf1", "my-config/conf2", "my-config/conf3"] def test_kwargs_listify(mock_init, monkeypatch): # Expected: use values from kwargs; each value resolved and listified new_path4 = "new1, new2" config = BaseAppConfiguration(path4=new_path4) assert config._raw_config["path4"] == "new1,new2" assert config.path4 == ["my-config/new1", "my-config/new2"] def test_kwargs_as_list_listify(mock_init, monkeypatch): # Expected: use values from kwargs; each value resolved and listified new_path4 = ["new1", "new2"] config = BaseAppConfiguration(path4=new_path4) assert config._raw_config["path4"] == ["new1", "new2"] assert config.path4 == ["my-config/new1", "my-config/new2"] @pytest.fixture def mock_check_against_root(mock_init, monkeypatch): def path_exists(_, path): return True if path == "root/foo" else False monkeypatch.setattr(BaseAppConfiguration, "_path_exists", path_exists) monkeypatch.setattr(BaseAppConfiguration, "_in_root_dir", lambda _, path: f"root/{path}") monkeypatch.setattr(BaseAppConfiguration, "paths_to_check_against_root", {"path1", "path4"}) def test_check_against_root_single_path(mock_check_against_root): # 1. Set path1='foo' # 2. It is resolved to 'my-config/foo' # 3. path1 is in paths to check against root # 4. 'my-config/foo' does not exist, so 'foo' is re-resolved w.r.t root # 5. 'root/foo' exists, so config.path1 is set to 'root/foo' config = BaseAppConfiguration(path1="foo") assert config.path1 == "root/foo" def test_check_against_root_list_of_paths(mock_check_against_root): # 1. Set path4='foo, bar' # 2. It is resolved to ['my-config/foo', 'my-config/bar'] # 3. path4 is in paths to check against root # 4. both paths do not exist, so both are re-resolved w.r.t root # 5. 'root/foo' exists, so config.path4 is set to ['root/foo', 'my-config/bar'] config = BaseAppConfiguration(path4="foo, bar") assert config.path4 == ["root/foo", "my-config/bar"] def test_set_alt_paths(mock_init, monkeypatch): def path_exists(_, path): return True if path == "foo" else False monkeypatch.setattr(BaseAppConfiguration, "_path_exists", path_exists) def reset_to_initial_default(): config.path1 = "my-config/my-config-files" config = BaseAppConfiguration() # default does not exist, one alt path exists assert config.path1 == "my-config/my-config-files" config._set_alt_paths("path1", "foo") assert config.path1 == "foo" # default does not exist, 2 alt paths passed, second exists reset_to_initial_default() config._set_alt_paths("path1", "invalid", "foo") assert config.path1 == "foo" # default does not exist, alt paths do not exist reset_to_initial_default() config._set_alt_paths("path1", "invalid", "invalid-2") assert config.path1 == "my-config/my-config-files"