mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-11-02 11:48:57 +08:00
John Chilton
5e00ffe0f6
The linking upload parameters will still be respected, but if none of them are set data fetch will default to just linking files during upload. This uses Dataset.external_filename instead of symlinks in the objectstore so that Galaxy has better tracking of the links and so this works closer to the way data libraries have always worked.
121 lines
3.2 KiB
Python
121 lines
3.2 KiB
Python
"""
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Test classes that should be shared between test scenarios.
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"""
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import os
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import shutil
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from tempfile import mkdtemp
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from typing import ClassVar
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from galaxy_test.driver.driver_util import GalaxyTestDriver
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REQUIRED_ROLE_EXPRESSION = "user@bx.psu.edu"
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GROUP_A = "fs_test_group"
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GROUP_B = "group name with spaces"
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REQUIRED_GROUP_EXPRESSION = f"{GROUP_A} or '{GROUP_B}'"
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def get_posix_file_source_config(
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root_dir: str, roles: str, groups: str, include_test_data_dir: bool, prefer_links: bool = False
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) -> str:
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rval = f"""
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- type: posix
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id: posix_test
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label: Posix
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doc: Files from local path
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root: {root_dir}
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writable: true
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requires_roles: {roles}
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requires_groups: {groups}
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"""
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if prefer_links:
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rval += f"""
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- type: posix
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id: linking_source
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label: Posix
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doc: Files from local path to links
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root: {root_dir}
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writable: true
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prefer_links: true
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"""
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if include_test_data_dir:
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rval += """
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- type: posix
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id: testdatafiles
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label: Galaxy Stock Test Data
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doc: Galaxy's test-data directory.
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root: test-data
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writable: false
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"""
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return rval
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def create_file_source_config_file_on(
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temp_dir,
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root_dir,
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include_test_data_dir,
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required_role_expression,
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required_group_expression,
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prefer_links: bool = False,
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):
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file_contents = get_posix_file_source_config(
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root_dir, required_role_expression, required_group_expression, include_test_data_dir, prefer_links=prefer_links
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)
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file_path = os.path.join(temp_dir, "file_sources_conf_posix.yml")
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with open(file_path, "w") as f:
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f.write(file_contents)
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return file_path
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class PosixFileSourceSetup:
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_test_driver: GalaxyTestDriver
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root_dir: str
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include_test_data_dir: ClassVar[bool] = False
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@classmethod
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def handle_galaxy_config_kwds(
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cls,
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config,
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clazz_=None,
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# Require role for access but do not require groups by default on every test to simplify them
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required_role_expression=REQUIRED_ROLE_EXPRESSION,
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required_group_expression="",
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prefer_links: bool = False,
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):
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temp_dir = os.path.realpath(mkdtemp())
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clazz_ = clazz_ or cls
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clazz_._test_driver.temp_directories.append(temp_dir)
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clazz_.root_dir = os.path.join(temp_dir, "root")
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file_sources_config_file = create_file_source_config_file_on(
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temp_dir,
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clazz_.root_dir,
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clazz_.include_test_data_dir,
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required_role_expression,
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required_group_expression,
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prefer_links=prefer_links,
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)
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config["file_sources_config_file"] = file_sources_config_file
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# Disable all stock plugins
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config["ftp_upload_dir"] = None
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config["library_import_dir"] = None
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config["user_library_import_dir"] = None
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def _write_file_fixtures(self):
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root = self.root_dir
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if os.path.exists(root):
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shutil.rmtree(root)
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os.mkdir(root)
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with open(os.path.join(root, "a"), "w") as f:
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f.write("a\n")
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subdir1 = os.path.join(root, "subdir1")
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os.mkdir(subdir1)
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with open(os.path.join(subdir1, "b"), "w") as f:
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f.write("b\n")
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return root
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