mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-11-04 05:42:12 +08:00
Nicola Soranzo
18dca18981
This required other changes included here as well: 1) Extend `parse_xml()` to accept a `Traversable` (i.e. the output of `resource_path()`. Open the file before passing it to `etree.parse()`, since lxml's implementation probably doesn't support a `Traversable`. This also simplifies the exception handling, since the workaround for the missing `errno` in the `OSError` exception is not needed any more. ------ 2) Fix Galaxy startup when the ``data_manager_config_file`` config option is set to an empty value When does this happen? ---------------------- planemo (which we use in the converters tests) set this option to an empty value when not testing data managers: https://github.com/galaxyproject/planemo/blob/master/planemo/galaxy/config.py#L452 This empty config value was resolved to the `path_resolves_to` directory for this option. With the change in 1) above, this results in the following traceback at Galaxy startup: ``` Traceback (most recent call last): File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 68, in app_pair app = galaxy.app.UniverseApplication(global_conf=global_conf, is_webapp=True, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/app.py", line 777, in __init__ self.data_managers = self._register_singleton(DataManagers) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/di.py", line 27, in _register_singleton instance = self[dep_type] ~~~~^^^^^^^^^^ File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 381, in __getitem__ return self.resolve(dep) ^^^^^^^^^^^^^^^^^ File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 265, in resolve return self._reflection_build_with_err_handling(dep_type, suppress_error) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 392, in _reflection_build_with_err_handling return self._reflection_build(dep_type) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.12/site-packages/lagom/container.py", line 408, in _reflection_build return dep_type(**sub_deps) # type: ignore ^^^^^^^^^^^^^^^^^^^^ File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/tools/data_manager/manager.py", line 44, in __init__ self.load_from_xml(filename) File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/tools/data_manager/manager.py", line 58, in load_from_xml tree = util.parse_xml(xml_filename) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/util/__init__.py", line 360, in parse_xml with source.open("rb") as f: ^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/pathlib.py", line 1013, in open return io.open(self, mode, buffering, encoding, errors, newline) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ IsADirectoryError: [Errno 21] Is a directory: '/tmp/tmps2qq5htq' ``` Why is this a problem now? -------------------------- Before this commit, `util.parse_xml()` was raising a `XMLSyntaxError` exception if passed a directory, but now it raises an `IsADirectoryError`, which is a subclass of `OSError` with errno 21. As a consequence, when `load_from_xml()` in lib/galaxy/tools/data_manager/manager.py calls `util.parse_xml()` passing a directory, the resulting exception is now re-raised in the `except OSError as e:` branch instead of just being logged, which is actually good since this is a misconfiguration. Solutions -------- - Do not resolve an empty/None path to the `path_resolves_to` directory. - Do not check empty/None paths against root - Adjst unit tests accordingly - Raise an OSError if the `job_config_file` config option is set to null (previously this would be resolved to a directory, also raising an OSError when trying to open that as a file). N.B.: This will also need to be fixed in Planemo by not setting the `data_manager_config_file` option when not needed.
281 lines
11 KiB
Python
281 lines
11 KiB
Python
from pathlib import Path
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import pytest
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from galaxy.config import BaseAppConfiguration
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from galaxy.config.schema import AppSchema
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MOCK_DEPRECATED_DIRS = {
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"my_config_dir": "old-config",
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"my_data_dir": "old-database",
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}
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# Mock properties loaded from schema (all options represent paths)
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MOCK_SCHEMA = {
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"my_config_dir": {
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"type": "str",
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"default": "my-config",
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},
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"my_data_dir": {
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"type": "str",
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"default": "my-data",
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},
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"path1": {
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"type": "str",
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"default": "my-config-files",
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"path_resolves_to": "my_config_dir",
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},
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"path2": {
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"type": "str",
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"default": "my-data-files",
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"path_resolves_to": "my_data_dir",
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},
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"path3": {
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"type": "str",
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"default": "my-other-files",
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},
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"path4": {
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"type": "str",
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"default": "conf1, conf2, conf3",
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"path_resolves_to": "my_config_dir",
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},
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}
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def get_schema(app_mapping):
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return {"mapping": {"_": {"mapping": app_mapping}}}
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@pytest.fixture
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def mock_init(monkeypatch):
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monkeypatch.setattr(BaseAppConfiguration, "_load_schema", lambda a: AppSchema(Path("no path"), "_"))
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monkeypatch.setattr(AppSchema, "_read_schema", lambda a, b: get_schema(MOCK_SCHEMA))
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monkeypatch.setattr(BaseAppConfiguration, "deprecated_dirs", MOCK_DEPRECATED_DIRS)
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monkeypatch.setattr(BaseAppConfiguration, "listify_options", {"path4"})
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def test_mock_schema_is_loaded(mock_init):
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# Check that mock is loaded as expected
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config = BaseAppConfiguration()
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assert len(config._raw_config) == 6
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assert config._raw_config["my_config_dir"] == "my-config"
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assert config._raw_config["my_data_dir"] == "my-data"
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assert config._raw_config["path1"] == "my-config-files"
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assert config._raw_config["path2"] == "my-data-files"
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assert config._raw_config["path3"] == "my-other-files"
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assert config._raw_config["path4"] == "conf1, conf2, conf3"
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def test_no_kwargs(mock_init):
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# Expected: use default from schema, then resolve
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config = BaseAppConfiguration()
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assert config.path1 == "my-config/my-config-files" # resolved
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assert config.path2 == "my-data/my-data-files" # resolved
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assert config.path3 == "my-other-files" # no change
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assert config.path4 == [
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"my-config/conf3"
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] # last value resolved and listified; others dropped as files do not exist
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def test_kwargs_relative_path(mock_init):
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# Expected: use value from kwargs, then resolve
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new_path1 = "foo1/bar"
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new_path2 = "foo2/bar"
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config = BaseAppConfiguration(path1=new_path1, path2=new_path2)
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assert config.path1 == "my-config/" + new_path1 # resolved
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assert config.path2 == "my-data/" + new_path2 # resolved
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assert config.path3 == "my-other-files" # no change
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def test_kwargs_absolute_path(mock_init):
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# Expected: use value from kwargs, do NOT resolve
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new_path1 = "/foo1/bar"
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new_path2 = "/foo2/bar"
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config = BaseAppConfiguration(path1=new_path1, path2=new_path2)
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assert config.path1 == new_path1 # NOT resolved
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assert config.path2 == new_path2 # NOT resolved
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assert config.path3 == "my-other-files" # no change
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def test_kwargs_relative_path_old_prefix(mock_init):
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# Expect: use value from kwargs, strip old prefix, then resolve
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new_path1 = "old-config/foo1/bar"
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new_path2 = "old-database/foo2/bar"
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config = BaseAppConfiguration(path1=new_path1, path2=new_path2)
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assert config.path1 == "my-config/foo1/bar" # stripped of old prefix, resolved
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assert config.path2 == "my-data/foo2/bar" # stripped of old prefix, resolved
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assert config.path3 == "my-other-files" # no change
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def test_kwargs_relative_path_old_prefix_csv_value(mock_init):
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# Expect: use value from kwargs, split at commas, then for each path strip
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# spaces, strip old prefix if needed, and resolve if needed
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config = BaseAppConfiguration(path4="old-config/foo/file1 , /foo1/bar, foo/file3")
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assert config.path4 == ["my-config/foo/file1", "/foo1/bar", "my-config/foo/file3"]
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def test_kwargs_relative_path_old_prefix_for_other_option(mock_init):
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# Expect: use value from kwargs, do NOT strip old prefix, then resolve
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# Reason: deprecated dirs are option-specific: we don't want to strip 'old-config'
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# (deprecated for the config_dir option) if it's used for another option
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new_path1 = "old-database/foo1/bar"
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new_path2 = "old-config/foo2/bar"
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config = BaseAppConfiguration(path1=new_path1, path2=new_path2)
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assert config.path1 == "my-config/" + new_path1 # resolved
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assert config.path2 == "my-data/" + new_path2 # resolved
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assert config.path3 == "my-other-files" # no change
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def test_kwargs_relative_path_old_prefix_empty_after_strip(mock_init):
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# Expect: use value from kwargs, strip old prefix, then resolve
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new_path1 = "old-config/foo"
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config = BaseAppConfiguration(path1=new_path1)
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assert config.path1 == "my-config/foo" # stripped of old prefix, then resolved
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assert config.path2 == "my-data/my-data-files" # stripped of old prefix, then resolved
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assert config.path3 == "my-other-files" # no change
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def test_kwargs_set_to_null(mock_init):
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# Expected: allow overriding with null
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# This is not a common scenario, but it does happen: one example is
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# `job_config` set to `None` when testing
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config = BaseAppConfiguration(path1=None)
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assert config.path1 is None
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assert config.path2 == "my-data/my-data-files" # resolved
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assert config.path3 == "my-other-files" # no change
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def test_add_sample_file(mock_init, monkeypatch):
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# Expected: sample file appended to list of defaults:
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# - resolved w.r.t sample-dir (_in_sample_dir mocked)
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# - has ".sample" suffix
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# Last value (sample file) resolved and listified; others dropped as files do not exist
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monkeypatch.setattr(BaseAppConfiguration, "add_sample_file_to_defaults", {"path1", "path4"})
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monkeypatch.setattr(BaseAppConfiguration, "_in_sample_dir", lambda a, path: f"/sample-dir/{path}")
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config = BaseAppConfiguration()
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assert config._raw_config["path1"] == "my-config-files"
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assert config.path1 == "/sample-dir/my-config-files.sample"
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assert config._raw_config["path4"] == "conf1, conf2, conf3"
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assert config.path4 == ["/sample-dir/conf3.sample"]
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def test_select_one_path_from_list(mock_init, monkeypatch):
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# Expected: files do not exist, so use last file in list (would be sample file); value is not a list
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monkeypatch.setattr(BaseAppConfiguration, "add_sample_file_to_defaults", {"path1"})
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monkeypatch.setattr(BaseAppConfiguration, "_in_sample_dir", lambda a, path: f"/sample-dir/{path}")
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config = BaseAppConfiguration()
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assert config._raw_config["path1"] == "my-config-files"
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assert config.path1 == "/sample-dir/my-config-files.sample"
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def test_select_one_path_from_list_all_files_exist(mock_init, monkeypatch):
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# Expected: all files exist, so use first file in list; value is not a list
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monkeypatch.setattr(BaseAppConfiguration, "add_sample_file_to_defaults", {"path1"})
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monkeypatch.setattr(BaseAppConfiguration, "_path_exists", lambda a, b: True)
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config = BaseAppConfiguration()
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assert config._raw_config["path1"] == "my-config-files"
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assert config.path1 == "my-config/my-config-files"
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def test_no_kwargs_listify(mock_init, monkeypatch):
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# Expected: last value resolved and listified; others dropped as files do not exist
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config = BaseAppConfiguration()
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assert config._raw_config["path4"] == "conf1, conf2, conf3"
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assert config.path4 == ["my-config/conf3"]
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def test_no_kwargs_listify_all_files_exist(mock_init, monkeypatch):
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# Expected: each value resolved and listified (mock: all files exist)
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monkeypatch.setattr(BaseAppConfiguration, "_path_exists", lambda a, b: True)
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config = BaseAppConfiguration()
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assert config._raw_config["path4"] == "conf1, conf2, conf3"
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assert config.path4 == ["my-config/conf1", "my-config/conf2", "my-config/conf3"]
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def test_kwargs_listify(mock_init, monkeypatch):
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# Expected: use values from kwargs; each value resolved and listified
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new_path4 = "new1, new2"
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config = BaseAppConfiguration(path4=new_path4)
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assert config._raw_config["path4"] == "new1,new2"
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assert config.path4 == ["my-config/new1", "my-config/new2"]
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def test_kwargs_as_list_listify(mock_init, monkeypatch):
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# Expected: use values from kwargs; each value resolved and listified
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new_path4 = ["new1", "new2"]
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config = BaseAppConfiguration(path4=new_path4)
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assert config._raw_config["path4"] == ["new1", "new2"]
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assert config.path4 == ["my-config/new1", "my-config/new2"]
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@pytest.fixture
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def mock_check_against_root(mock_init, monkeypatch):
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def path_exists(_, path):
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return True if path == "root/foo" else False
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monkeypatch.setattr(BaseAppConfiguration, "_path_exists", path_exists)
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monkeypatch.setattr(BaseAppConfiguration, "_in_root_dir", lambda _, path: f"root/{path}")
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monkeypatch.setattr(BaseAppConfiguration, "paths_to_check_against_root", {"path1", "path4"})
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def test_check_against_root_single_path(mock_check_against_root):
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# 1. Set path1='foo'
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# 2. It is resolved to 'my-config/foo'
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# 3. path1 is in paths to check against root
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# 4. 'my-config/foo' does not exist, so 'foo' is re-resolved w.r.t root
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# 5. 'root/foo' exists, so config.path1 is set to 'root/foo'
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config = BaseAppConfiguration(path1="foo")
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assert config.path1 == "root/foo"
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def test_check_against_root_list_of_paths(mock_check_against_root):
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# 1. Set path4='foo, bar'
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# 2. It is resolved to ['my-config/foo', 'my-config/bar']
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# 3. path4 is in paths to check against root
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# 4. both paths do not exist, so both are re-resolved w.r.t root
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# 5. 'root/foo' exists, so config.path4 is set to ['root/foo', 'my-config/bar']
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config = BaseAppConfiguration(path4="foo, bar")
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assert config.path4 == ["root/foo", "my-config/bar"]
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def test_set_alt_paths(mock_init, monkeypatch):
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def path_exists(_, path):
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return True if path == "foo" else False
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monkeypatch.setattr(BaseAppConfiguration, "_path_exists", path_exists)
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def reset_to_initial_default():
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config.path1 = "my-config/my-config-files"
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config = BaseAppConfiguration()
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# default does not exist, one alt path exists
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assert config.path1 == "my-config/my-config-files"
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config._set_alt_paths("path1", "foo")
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assert config.path1 == "foo"
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# default does not exist, 2 alt paths passed, second exists
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reset_to_initial_default()
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config._set_alt_paths("path1", "invalid", "foo")
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assert config.path1 == "foo"
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# default does not exist, alt paths do not exist
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reset_to_initial_default()
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config._set_alt_paths("path1", "invalid", "invalid-2")
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assert config.path1 == "my-config/my-config-files"
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