Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

galaxy.tool_util.verify package

Module of utilities for verifying test results.

galaxy.tool_util.verify.verify(item_label: str, output_content: bytes, attributes: Dict[str, Any], filename: Optional[str] = None, get_filecontent: Optional[Callable[[str], bytes]] = None, get_filename: Optional[Callable[[str], str]] = None, keep_outputs_dir: Optional[str] = None, verify_extra_files: Optional[Callable] = None, mode='file')[source]

Verify the content of a test output using test definitions described by attributes.

Throw an informative assertion error if any of these tests fail.

galaxy.tool_util.verify.make_temp_fname(fname=None)[source]

Safe temp name - preserve the file extension for tools that interpret it.

galaxy.tool_util.verify.files_delta(file1, file2, attributes=None)[source]

Check the contents of 2 files for size differences.

galaxy.tool_util.verify.get_compressed_formats(attributes)[source]
galaxy.tool_util.verify.files_diff(file1, file2, attributes=None)[source]

Check the contents of 2 files for differences.

galaxy.tool_util.verify.files_re_match(file1, file2, attributes=None)[source]

Check the contents of 2 files for differences using re.match.

galaxy.tool_util.verify.files_re_match_multiline(file1, file2, attributes=None)[source]

Check the contents of 2 files for differences using re.match in multiline mode.

galaxy.tool_util.verify.files_contains(file1, file2, attributes=None)[source]

Check the contents of file2 for substrings found in file1, on a per-line basis.

Subpackages

Submodules

galaxy.tool_util.verify.interactor module

class galaxy.tool_util.verify.interactor.OutputsDict[source]

Bases: dict

Ordered dict that can also be accessed by index.

>>> out = OutputsDict()
>>> out['item1'] = 1
>>> out['item2'] = 2
>>> out[1] == 2 == out['item2']
True
class galaxy.tool_util.verify.interactor.ValidToolTestDict[source]

Bases: TypedDict

inputs: Any
outputs: Any
output_collections: List[Dict[str, Any]]
stdout: typing_extensions.NotRequired[Optional[List[AssertionDict]]]
stderr: typing_extensions.NotRequired[Optional[List[AssertionDict]]]
expect_exit_code: typing_extensions.NotRequired[int]
expect_failure: typing_extensions.NotRequired[bool]
expect_test_failure: typing_extensions.NotRequired[bool]
maxseconds: typing_extensions.NotRequired[int]
num_outputs: typing_extensions.NotRequired[int]
command_line: typing_extensions.NotRequired[Optional[List[AssertionDict]]]
command_version: typing_extensions.NotRequired[Optional[List[AssertionDict]]]
required_files: typing_extensions.NotRequired[List[Any]]
required_data_tables: typing_extensions.NotRequired[List[Any]]
required_loc_files: typing_extensions.NotRequired[List[str]]
error: typing_extensions.Literal[False]
tool_id: str
tool_version: str
test_index: int
class galaxy.tool_util.verify.interactor.InvalidToolTestDict[source]

Bases: TypedDict

error: typing_extensions.Literal[True]
tool_id: str
tool_version: str
test_index: int
inputs: Any
exception: str
maxseconds: Optional[int]
galaxy.tool_util.verify.interactor.stage_data_in_history(galaxy_interactor: GalaxyInteractorApi, tool_id: str, all_test_data, history=None, force_path_paste=False, maxseconds=86400, tool_version=None)[source]
class galaxy.tool_util.verify.interactor.RunToolResponse(inputs, outputs, output_collections, jobs)[source]

Bases: tuple

property inputs

Alias for field number 0

property outputs

Alias for field number 1

property output_collections

Alias for field number 2

property jobs

Alias for field number 3

class galaxy.tool_util.verify.interactor.GalaxyInteractorApi(**kwds)[source]

Bases: object

__init__(**kwds)[source]
cookies: Optional[RequestsCookieJar]
api_key: Optional[str]
keep_outputs_dir: Optional[str]
property target_galaxy_version
property supports_test_data_download
get_tests_summary()[source]
get_tool_tests(tool_id: str, tool_version: Optional[str] = None) List[Union[ValidToolTestDict, InvalidToolTestDict]][source]
verify_output_collection(output_collection_def, output_collection_id, history, tool_id, tool_version=None)[source]
verify_output(history_id, jobs, output_data, output_testdef, tool_id, maxseconds, tool_version=None)[source]
wait_for_jobs(history_id, jobs, maxseconds)[source]
verify_output_dataset(history_id, hda_id, outfile, attributes, tool_id, tool_version=None)[source]
wait_for_job(job_id, history_id=None, maxseconds=86400)[source]
wait_for(func, what='tool test run', **kwd)[source]
get_job_stdio(job_id)[source]
get_history(history_name='test_history')[source]
test_history(require_new: bool = True, cleanup_callback: Optional[Callable[[str], None]] = None) Generator[str, None, None][source]
new_history(history_name='test_history', publish_history=False)[source]
publish_history(history_id)[source]
test_data_path(tool_id, filename, tool_version=None)[source]
test_data_download(tool_id, filename, mode='file', is_output=True, tool_version=None)[source]
stage_data_async(test_data: Dict[str, Any], history_id: str, tool_id: str, force_path_paste: bool = False, maxseconds: int = 86400, tool_version: Optional[str] = None) Callable[[], None][source]
run_tool(testdef, history_id, resource_parameters=None) RunToolResponse[source]
output_hid(output_data)[source]
delete_history(history)[source]
format_for_summary(blob, empty_message, prefix='|  ')[source]
ensure_user_with_email(email, password=None)[source]
api_key_header(key: Optional[str], admin: bool, anon: bool, headers: Optional[Dict[str, Optional[str]]]) Dict[str, Optional[str]][source]
get_api_url(path: str) str[source]
galaxy.tool_util.verify.interactor.prepare_request_params(data: Optional[Dict[str, Any]] = None, files: Optional[Dict[str, Any]] = None, as_json: bool = False, params: Optional[Dict[str, Any]] = None, headers: Optional[Dict[str, Optional[str]]] = None, cookies: Optional[RequestsCookieJar] = None) Dict[str, Any][source]
galaxy.tool_util.verify.interactor.ensure_tool_run_response_okay(submit_response_object, request_desc, inputs=None)[source]
exception galaxy.tool_util.verify.interactor.RunToolException(message, inputs=None, dynamic_param_error=False)[source]

Bases: Exception

__init__(message, inputs=None, dynamic_param_error=False)[source]
galaxy.tool_util.verify.interactor.verify_hid(filename: Optional[str], hda_id: str, attributes: Dict[str, Any], test_data_downloader, dataset_fetcher=None, keep_outputs_dir: Optional[str] = None)[source]
galaxy.tool_util.verify.interactor.verify_collection(output_collection_def, data_collection, verify_dataset)[source]
class galaxy.tool_util.verify.interactor.TestConfig(*args, **kwds)[source]

Bases: Protocol

get_test_config(job_data: Dict[str, Any]) Optional[Dict[str, Any]][source]
__init__(*args, **kwargs)
class galaxy.tool_util.verify.interactor.NullClientTestConfig(*args, **kwds)[source]

Bases: TestConfig

get_test_config(job_data)[source]
class galaxy.tool_util.verify.interactor.DictClientTestConfig(*args, **kwds)[source]

Bases: TestConfig

__init__(tools)[source]
get_test_config(job_data)[source]
galaxy.tool_util.verify.interactor.verify_tool(tool_id: str, galaxy_interactor: GalaxyInteractorApi, resource_parameters: Optional[Dict[str, Any]] = None, register_job_data: Optional[Callable[[Dict[str, Any]], None]] = None, test_index: int = 0, tool_version: Optional[str] = None, quiet: bool = False, test_history: Optional[str] = None, no_history_cleanup: bool = False, publish_history: bool = False, force_path_paste: bool = False, maxseconds: int = 86400, client_test_config: Optional[TestConfig] = None, skip_with_reference_data: bool = False, skip_on_dynamic_param_errors: bool = False, _tool_test_dicts: Optional[List[Union[ValidToolTestDict, InvalidToolTestDict]]] = None)[source]
exception galaxy.tool_util.verify.interactor.JobOutputsError(output_exceptions, job_stdio)[source]

Bases: AssertionError

__init__(output_exceptions, job_stdio)[source]
class galaxy.tool_util.verify.interactor.ToolTestDescription(processed_test_dict: Union[ValidToolTestDict, InvalidToolTestDict])[source]

Bases: object

Encapsulates information about a tool test, and allows creation of a dynamic TestCase class (the unittest framework is very class oriented, doing dynamic tests in this way allows better integration)

__init__(processed_test_dict: Union[ValidToolTestDict, InvalidToolTestDict])[source]
test_data()[source]

Iterator over metadata representing the required files for upload.

to_dict()[source]
galaxy.tool_util.verify.interactor.test_data_iter(required_files)[source]

galaxy.tool_util.verify.script module

class galaxy.tool_util.verify.script.TestReference(tool_id, tool_version, test_index)[source]

Bases: tuple

property tool_id

Alias for field number 0

property tool_version

Alias for field number 1

property test_index

Alias for field number 2

class galaxy.tool_util.verify.script.TestException(tool_id, exception, was_recorded)[source]

Bases: tuple

property tool_id

Alias for field number 0

property exception

Alias for field number 1

property was_recorded

Alias for field number 2

class galaxy.tool_util.verify.script.Results(default_suitename: str, test_json: str, append: bool = False, galaxy_url: Optional[str] = None)[source]

Bases: object

__init__(default_suitename: str, test_json: str, append: bool = False, galaxy_url: Optional[str] = None) None[source]
test_exceptions: List[TestException]
register_result(result: Dict[str, Any]) None[source]
register_exception(test_exception: TestException) None[source]
already_successful(test_reference: TestReference) bool[source]
already_executed(test_reference: TestReference) bool[source]
write() None[source]
info_message() str[source]
galaxy.tool_util.verify.script.test_tools(galaxy_interactor: GalaxyInteractorApi, test_references: List[TestReference], results: Results, log: Optional[Logger] = None, parallel_tests: int = 1, history_per_test_case: bool = False, history_name: Optional[str] = None, no_history_reuse: bool = False, no_history_cleanup: bool = False, publish_history: bool = False, retries: int = 0, verify_kwds: Optional[Dict[str, Any]] = None) None[source]

Run through tool tests and write report.

galaxy.tool_util.verify.script.build_case_references(galaxy_interactor: GalaxyInteractorApi, tool_id: str = '*', tool_version: Optional[str] = None, test_index: int = -1, page_size: int = 0, page_number: int = 0, test_filters: Optional[List[Callable[[TestReference], bool]]] = None, log: Optional[Logger] = None) List[TestReference][source]
galaxy.tool_util.verify.script.main(argv=None) None[source]
galaxy.tool_util.verify.script.run_tests(args: Namespace, test_filters: Optional[List[Callable[[TestReference], bool]]] = None, log: Optional[Logger] = None) None[source]
galaxy.tool_util.verify.script.setup_global_logger(name: str, log_file: Optional[str] = None, verbose: bool = False) Logger[source]
galaxy.tool_util.verify.script.arg_parser() ArgumentParser[source]

galaxy.tool_util.verify.test_data module

class galaxy.tool_util.verify.test_data.TestDataResolver(file_dirs=None, env_var='GALAXY_TEST_FILE_DIR', environ=environ({'JAVA_HOME': '/usr/lib/jvm/temurin-11-jdk-amd64', 'LEIN_HOME': '/usr/local/lib/lein', 'GHCUP_INSTALL_BASE_PREFIX': '/usr/local', 'RUNNER_NAME': 'GitHub Actions 33', 'STATS_BLT': 'true', 'GITHUB_REF_NAME': 'release_23.2', 'ACCEPT_EULA': 'Y', 'DOTNET_SKIP_FIRST_TIME_EXPERIENCE': '1', 'GITHUB_ENV': '/home/runner/work/_temp/_runner_file_commands/set_env_5f883a29-aa2b-477f-8850-dac80990cd00', 'STATS_RDCL': 'true', 'GITHUB_REPOSITORY_ID': '31211061', 'RUNNER_TRACKING_ID': 'github_534f5e32-9168-4fc9-9cbe-a208096807fd', 'GITHUB_REPOSITORY_OWNER': 'galaxyproject', 'NVM_DIR': '/home/runner/.nvm', 'JAVA_HOME_17_X64': '/usr/lib/jvm/temurin-17-jdk-amd64', 'GITHUB_EVENT_NAME': 'push', 'SGX_AESM_ADDR': '1', 'PWD': '/home/runner/work/galaxy/galaxy', 'GITHUB_ACTION_REPOSITORY': '', 'RUNNER_WORKSPACE': '/home/runner/work/galaxy', 'GITHUB_WORKFLOW_SHA': '4a845a4b46cc8253713c64d774905e1b38276e64', 'RUNNER_OS': 'Linux', 'EDGEWEBDRIVER': '/usr/local/share/edge_driver', 'CI': 'true', 'LANG': 'C.UTF-8', 'RUNNER_TEMP': '/home/runner/work/_temp', 'GITHUB_SERVER_URL': 'https://github.com', 'STATS_TRP': 'true', 'PERFLOG_LOCATION_SETTING': 'RUNNER_PERFLOG', 'RUNNER_USER': 'runner', 'GITHUB_API_URL': 'https://api.github.com', 'MAKEFLAGS': 'w', 'CHROME_BIN': '/usr/bin/google-chrome', 'PKG_CONFIG_PATH': '/opt/hostedtoolcache/Python/3.7.17/x64/lib/pkgconfig', 'Python2_ROOT_DIR': '/opt/hostedtoolcache/Python/3.7.17/x64', 'GITHUB_SHA': '4a845a4b46cc8253713c64d774905e1b38276e64', 'ANDROID_NDK_HOME': '/usr/local/lib/android/sdk/ndk/27.1.12297006', 'GITHUB_ACTOR_ID': '6804901', 'POWERSHELL_DISTRIBUTION_CHANNEL': 'GitHub-Actions-ubuntu22', 'SELENIUM_JAR_PATH': '/usr/share/java/selenium-server.jar', 'GOROOT_1_21_X64': '/opt/hostedtoolcache/go/1.21.13/x64', 'pythonLocation': '/opt/hostedtoolcache/Python/3.7.17/x64', 'MFLAGS': '-w', 'ANDROID_NDK_LATEST_HOME': '/usr/local/lib/android/sdk/ndk/27.1.12297006', 'STATS_EXT': 'true', 'BOOTSTRAP_HASKELL_NONINTERACTIVE': '1', 'JAVA_HOME_8_X64': '/usr/lib/jvm/temurin-8-jdk-amd64', 'PIPX_HOME': '/opt/pipx', 'STATS_TIS': 'mining', 'GITHUB_RUN_ATTEMPT': '1', 'RUNNER_PERFLOG': '/home/runner/perflog', 'GITHUB_TRIGGERING_ACTOR': 'mvdbeek', 'DOTNET_NOLOGO': '1', 'DOTNET_MULTILEVEL_LOOKUP': '0', 'JAVA_HOME_11_X64': '/usr/lib/jvm/temurin-11-jdk-amd64', 'GITHUB_REF': 'refs/heads/release_23.2', 'GITHUB_RUN_NUMBER': '24253', 'Python3_ROOT_DIR': '/opt/hostedtoolcache/Python/3.7.17/x64', 'ANDROID_SDK_ROOT': '/usr/local/lib/android/sdk', 'GITHUB_JOB': 'build', 'ANDROID_HOME': '/usr/local/lib/android/sdk', 'LD_LIBRARY_PATH': '/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/pylibmagic:/opt/hostedtoolcache/Python/3.7.17/x64/lib', 'GITHUB_STATE': '/home/runner/work/_temp/_runner_file_commands/save_state_5f883a29-aa2b-477f-8850-dac80990cd00', 'SHLVL': '1', 'ANDROID_NDK': '/usr/local/lib/android/sdk/ndk/27.1.12297006', 'ImageVersion': '20240915.1.0', 'PATH': '/opt/hostedtoolcache/Python/3.7.17/x64/bin:/opt/hostedtoolcache/Python/3.7.17/x64:/snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin', 'LEIN_JAR': '/usr/local/lib/lein/self-installs/leiningen-2.11.2-standalone.jar', 'GITHUB_EVENT_PATH': '/home/runner/work/_temp/_github_workflow/event.json', 'STATS_D': 'false', 'STATS_D_D': 'false', 'STATS_UE': 'true', 'GRADLE_HOME': '/usr/share/gradle-8.10.1', 'GITHUB_RETENTION_DAYS': '90', 'INVOCATION_ID': '0d269066c0d1481297d3069910adcedc', 'XDG_CONFIG_HOME': '/home/runner/.config', 'GITHUB_ACTIONS': 'true', 'GITHUB_WORKFLOW_REF': 'galaxyproject/galaxy/.github/workflows/docs.yaml@refs/heads/release_23.2', 'CONDA': '/usr/share/miniconda', 'GITHUB_HEAD_REF': '', 'STATS_EXTP': 'https://provjobdsettingscdn.blob.core.windows.net/settings/provjobdsettings-0.5.189/provjobd.data', 'CHROMEWEBDRIVER': '/usr/local/share/chromedriver-linux64', 'PIPX_BIN_DIR': '/opt/pipx_bin', 'GITHUB_REF_PROTECTED': 'true', 'DEPLOYMENT_BASEPATH': '/opt/runner', 'GITHUB_REF_TYPE': 'branch', 'GECKOWEBDRIVER': '/usr/local/share/gecko_driver', 'SYSTEMD_EXEC_PID': '606', 'GITHUB_ACTION_REF': '', 'GITHUB_WORKSPACE': '/home/runner/work/galaxy/galaxy', 'USER': 'runner', 'SWIFT_PATH': '/usr/share/swift/usr/bin', 'STATS_VMD': 'true', 'GITHUB_STEP_SUMMARY': '/home/runner/work/_temp/_runner_file_commands/step_summary_5f883a29-aa2b-477f-8850-dac80990cd00', 'RUNNER_ARCH': 'X64', 'GITHUB_PATH': '/home/runner/work/_temp/_runner_file_commands/add_path_5f883a29-aa2b-477f-8850-dac80990cd00', 'RUNNER_TOOL_CACHE': '/opt/hostedtoolcache', '_': '/usr/bin/make', 'ANDROID_NDK_ROOT': '/usr/local/lib/android/sdk/ndk/27.1.12297006', 'XDG_RUNTIME_DIR': '/run/user/1001', 'AGENT_TOOLSDIRECTORY': '/opt/hostedtoolcache', 'GITHUB_REPOSITORY': 'galaxyproject/galaxy', 'VCPKG_INSTALLATION_ROOT': '/usr/local/share/vcpkg', 'JOURNAL_STREAM': '8:4491', 'GITHUB_ACTION': '__run_8', 'DEBIAN_FRONTEND': 'noninteractive', 'HOME': '/home/runner', 'GITHUB_GRAPHQL_URL': 'https://api.github.com/graphql', 'GITHUB_WORKFLOW': 'Build docs', 'GOROOT_1_20_X64': '/opt/hostedtoolcache/go/1.20.14/x64', 'GITHUB_RUN_ID': '10954649823', 'HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS': '3650', 'GITHUB_ACTOR': 'mvdbeek', 'ANT_HOME': '/usr/share/ant', 'ImageOS': 'ubuntu22', 'Python_ROOT_DIR': '/opt/hostedtoolcache/Python/3.7.17/x64', 'ACTIONS_RUNNER_ACTION_ARCHIVE_CACHE': '/opt/actionarchivecache', 'TARGET_BRANCH': 'release_23.2', 'GITHUB_OUTPUT': '/home/runner/work/_temp/_runner_file_commands/set_output_5f883a29-aa2b-477f-8850-dac80990cd00', 'GITHUB_BASE_REF': '', 'STATS_V3PS': 'true', 'GITHUB_REPOSITORY_OWNER_ID': '7937847', 'GOROOT_1_22_X64': '/opt/hostedtoolcache/go/1.22.7/x64', 'AZURE_EXTENSION_DIR': '/opt/az/azcliextensions', 'RUNNER_ENVIRONMENT': 'github-hosted', 'STATS_VMFE': 'true', 'HOMEBREW_NO_AUTO_UPDATE': '1', 'JAVA_HOME_21_X64': '/usr/lib/jvm/temurin-21-jdk-amd64', 'MAKELEVEL': '2', 'DOCUTILSCONFIG': '/home/runner/work/galaxy/galaxy/doc/source/docutils.conf', 'LIBRARY_PATH': '/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/pylibmagic:', 'MAGIC': '/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/pylibmagic/magic.mgc:'}))[source]

Bases: object

__init__(file_dirs=None, env_var='GALAXY_TEST_FILE_DIR', environ=environ({'JAVA_HOME': '/usr/lib/jvm/temurin-11-jdk-amd64', 'LEIN_HOME': '/usr/local/lib/lein', 'GHCUP_INSTALL_BASE_PREFIX': '/usr/local', 'RUNNER_NAME': 'GitHub Actions 33', 'STATS_BLT': 'true', 'GITHUB_REF_NAME': 'release_23.2', 'ACCEPT_EULA': 'Y', 'DOTNET_SKIP_FIRST_TIME_EXPERIENCE': '1', 'GITHUB_ENV': '/home/runner/work/_temp/_runner_file_commands/set_env_5f883a29-aa2b-477f-8850-dac80990cd00', 'STATS_RDCL': 'true', 'GITHUB_REPOSITORY_ID': '31211061', 'RUNNER_TRACKING_ID': 'github_534f5e32-9168-4fc9-9cbe-a208096807fd', 'GITHUB_REPOSITORY_OWNER': 'galaxyproject', 'NVM_DIR': '/home/runner/.nvm', 'JAVA_HOME_17_X64': '/usr/lib/jvm/temurin-17-jdk-amd64', 'GITHUB_EVENT_NAME': 'push', 'SGX_AESM_ADDR': '1', 'PWD': '/home/runner/work/galaxy/galaxy', 'GITHUB_ACTION_REPOSITORY': '', 'RUNNER_WORKSPACE': '/home/runner/work/galaxy', 'GITHUB_WORKFLOW_SHA': '4a845a4b46cc8253713c64d774905e1b38276e64', 'RUNNER_OS': 'Linux', 'EDGEWEBDRIVER': '/usr/local/share/edge_driver', 'CI': 'true', 'LANG': 'C.UTF-8', 'RUNNER_TEMP': '/home/runner/work/_temp', 'GITHUB_SERVER_URL': 'https://github.com', 'STATS_TRP': 'true', 'PERFLOG_LOCATION_SETTING': 'RUNNER_PERFLOG', 'RUNNER_USER': 'runner', 'GITHUB_API_URL': 'https://api.github.com', 'MAKEFLAGS': 'w', 'CHROME_BIN': '/usr/bin/google-chrome', 'PKG_CONFIG_PATH': '/opt/hostedtoolcache/Python/3.7.17/x64/lib/pkgconfig', 'Python2_ROOT_DIR': '/opt/hostedtoolcache/Python/3.7.17/x64', 'GITHUB_SHA': '4a845a4b46cc8253713c64d774905e1b38276e64', 'ANDROID_NDK_HOME': '/usr/local/lib/android/sdk/ndk/27.1.12297006', 'GITHUB_ACTOR_ID': '6804901', 'POWERSHELL_DISTRIBUTION_CHANNEL': 'GitHub-Actions-ubuntu22', 'SELENIUM_JAR_PATH': '/usr/share/java/selenium-server.jar', 'GOROOT_1_21_X64': '/opt/hostedtoolcache/go/1.21.13/x64', 'pythonLocation': '/opt/hostedtoolcache/Python/3.7.17/x64', 'MFLAGS': '-w', 'ANDROID_NDK_LATEST_HOME': '/usr/local/lib/android/sdk/ndk/27.1.12297006', 'STATS_EXT': 'true', 'BOOTSTRAP_HASKELL_NONINTERACTIVE': '1', 'JAVA_HOME_8_X64': '/usr/lib/jvm/temurin-8-jdk-amd64', 'PIPX_HOME': '/opt/pipx', 'STATS_TIS': 'mining', 'GITHUB_RUN_ATTEMPT': '1', 'RUNNER_PERFLOG': '/home/runner/perflog', 'GITHUB_TRIGGERING_ACTOR': 'mvdbeek', 'DOTNET_NOLOGO': '1', 'DOTNET_MULTILEVEL_LOOKUP': '0', 'JAVA_HOME_11_X64': '/usr/lib/jvm/temurin-11-jdk-amd64', 'GITHUB_REF': 'refs/heads/release_23.2', 'GITHUB_RUN_NUMBER': '24253', 'Python3_ROOT_DIR': '/opt/hostedtoolcache/Python/3.7.17/x64', 'ANDROID_SDK_ROOT': '/usr/local/lib/android/sdk', 'GITHUB_JOB': 'build', 'ANDROID_HOME': '/usr/local/lib/android/sdk', 'LD_LIBRARY_PATH': '/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/pylibmagic:/opt/hostedtoolcache/Python/3.7.17/x64/lib', 'GITHUB_STATE': '/home/runner/work/_temp/_runner_file_commands/save_state_5f883a29-aa2b-477f-8850-dac80990cd00', 'SHLVL': '1', 'ANDROID_NDK': '/usr/local/lib/android/sdk/ndk/27.1.12297006', 'ImageVersion': '20240915.1.0', 'PATH': '/opt/hostedtoolcache/Python/3.7.17/x64/bin:/opt/hostedtoolcache/Python/3.7.17/x64:/snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin', 'LEIN_JAR': '/usr/local/lib/lein/self-installs/leiningen-2.11.2-standalone.jar', 'GITHUB_EVENT_PATH': '/home/runner/work/_temp/_github_workflow/event.json', 'STATS_D': 'false', 'STATS_D_D': 'false', 'STATS_UE': 'true', 'GRADLE_HOME': '/usr/share/gradle-8.10.1', 'GITHUB_RETENTION_DAYS': '90', 'INVOCATION_ID': '0d269066c0d1481297d3069910adcedc', 'XDG_CONFIG_HOME': '/home/runner/.config', 'GITHUB_ACTIONS': 'true', 'GITHUB_WORKFLOW_REF': 'galaxyproject/galaxy/.github/workflows/docs.yaml@refs/heads/release_23.2', 'CONDA': '/usr/share/miniconda', 'GITHUB_HEAD_REF': '', 'STATS_EXTP': 'https://provjobdsettingscdn.blob.core.windows.net/settings/provjobdsettings-0.5.189/provjobd.data', 'CHROMEWEBDRIVER': '/usr/local/share/chromedriver-linux64', 'PIPX_BIN_DIR': '/opt/pipx_bin', 'GITHUB_REF_PROTECTED': 'true', 'DEPLOYMENT_BASEPATH': '/opt/runner', 'GITHUB_REF_TYPE': 'branch', 'GECKOWEBDRIVER': '/usr/local/share/gecko_driver', 'SYSTEMD_EXEC_PID': '606', 'GITHUB_ACTION_REF': '', 'GITHUB_WORKSPACE': '/home/runner/work/galaxy/galaxy', 'USER': 'runner', 'SWIFT_PATH': '/usr/share/swift/usr/bin', 'STATS_VMD': 'true', 'GITHUB_STEP_SUMMARY': '/home/runner/work/_temp/_runner_file_commands/step_summary_5f883a29-aa2b-477f-8850-dac80990cd00', 'RUNNER_ARCH': 'X64', 'GITHUB_PATH': '/home/runner/work/_temp/_runner_file_commands/add_path_5f883a29-aa2b-477f-8850-dac80990cd00', 'RUNNER_TOOL_CACHE': '/opt/hostedtoolcache', '_': '/usr/bin/make', 'ANDROID_NDK_ROOT': '/usr/local/lib/android/sdk/ndk/27.1.12297006', 'XDG_RUNTIME_DIR': '/run/user/1001', 'AGENT_TOOLSDIRECTORY': '/opt/hostedtoolcache', 'GITHUB_REPOSITORY': 'galaxyproject/galaxy', 'VCPKG_INSTALLATION_ROOT': '/usr/local/share/vcpkg', 'JOURNAL_STREAM': '8:4491', 'GITHUB_ACTION': '__run_8', 'DEBIAN_FRONTEND': 'noninteractive', 'HOME': '/home/runner', 'GITHUB_GRAPHQL_URL': 'https://api.github.com/graphql', 'GITHUB_WORKFLOW': 'Build docs', 'GOROOT_1_20_X64': '/opt/hostedtoolcache/go/1.20.14/x64', 'GITHUB_RUN_ID': '10954649823', 'HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS': '3650', 'GITHUB_ACTOR': 'mvdbeek', 'ANT_HOME': '/usr/share/ant', 'ImageOS': 'ubuntu22', 'Python_ROOT_DIR': '/opt/hostedtoolcache/Python/3.7.17/x64', 'ACTIONS_RUNNER_ACTION_ARCHIVE_CACHE': '/opt/actionarchivecache', 'TARGET_BRANCH': 'release_23.2', 'GITHUB_OUTPUT': '/home/runner/work/_temp/_runner_file_commands/set_output_5f883a29-aa2b-477f-8850-dac80990cd00', 'GITHUB_BASE_REF': '', 'STATS_V3PS': 'true', 'GITHUB_REPOSITORY_OWNER_ID': '7937847', 'GOROOT_1_22_X64': '/opt/hostedtoolcache/go/1.22.7/x64', 'AZURE_EXTENSION_DIR': '/opt/az/azcliextensions', 'RUNNER_ENVIRONMENT': 'github-hosted', 'STATS_VMFE': 'true', 'HOMEBREW_NO_AUTO_UPDATE': '1', 'JAVA_HOME_21_X64': '/usr/lib/jvm/temurin-21-jdk-amd64', 'MAKELEVEL': '2', 'DOCUTILSCONFIG': '/home/runner/work/galaxy/galaxy/doc/source/docutils.conf', 'LIBRARY_PATH': '/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/pylibmagic:', 'MAGIC': '/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/pylibmagic/magic.mgc:'}))[source]
get_filename(name: str) str[source]
get_filecontent(name: str) bytes[source]
get_directory(name: str) str[source]
exception galaxy.tool_util.verify.test_data.TestDataNotFoundError[source]

Bases: ValueError

galaxy.tool_util.verify.test_data.build_resolver(uri: str, environ)[source]
class galaxy.tool_util.verify.test_data.FileDataResolver(file_dir: str)[source]

Bases: object

__init__(file_dir: str)[source]
exists(filename: str)[source]
path(filename: str)[source]
class galaxy.tool_util.verify.test_data.GitDataResolver(repository: str, environ)[source]

Bases: FileDataResolver

__init__(repository: str, environ)[source]
exists(filename: str)[source]
update_repository()[source]
execute(cmd)[source]

galaxy.tool_util.verify.wait module

Abstraction for waiting on API conditions to become true.

galaxy.tool_util.verify.wait.wait_on(function: Callable, desc: str, timeout: Union[int, float], delta: Union[int, float] = 0.25, polling_backoff: Union[int, float] = 0, sleep_: Optional[Callable] = None)[source]

Wait for function to return non-None value.

Grow the polling interval (initially delta defaulting to 0.25 seconds) incrementally by the supplied polling_backoff (defaulting to 0).

Throw a TimeoutAssertionError if the supplied timeout is reached without supplied function ever returning a non-None value.

exception galaxy.tool_util.verify.wait.TimeoutAssertionError(message)[source]

Bases: AssertionError

Derivative of AssertionError indicating wait_on exceeded max time.

__init__(message)[source]