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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] | None, filename: str | None = None, get_filecontent: Callable[[str], bytes] | None = None, get_filename: Callable[[str], str] | None = None, keep_outputs_dir: str | None = None, verify_extra_files: Callable | None = 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.

galaxy.tool_util.verify.intersection_over_union(mask1: numpy.typing.NDArray, mask2: numpy.typing.NDArray, pin_labels: List[int] | None = None) → numpy.floating[source]

Compute the intersection over union (IoU) for the objects in two masks containing lables.

The IoU is computed for each uniquely labeled image region (object), and the overall minimum value is returned (i.e. the worst value). To compute the IoU for each object, the corresponding object in the other mask needs to be determined. The object correspondences are not necessarily symmetric.

By default, the corresponding object in the other mask is determined as the one with the largest IoU value. If the label of an object is listed in pin_labels, then the corresponding object in the other mask is determined as the object with the same label value. Objects with labels listed in pin_labels also cannot correspond to objects with different labels. This is particularly useful when specific image regions must always be labeled with a designated label value (e.g., the image background is often labeled with 0 or -1).

galaxy.tool_util.verify.get_image_metric(attributes: Dict[str, Any]) → Callable[[numpy.typing.NDArray, numpy.typing.NDArray], numpy.floating][source]

galaxy.tool_util.verify.files_image_diff(file1: str, file2: str, attributes: Dict[str, Any] | None = None) → None[source]: Check the pixel data of 2 image files for differences.

Subpackages

galaxy.tool_util.verify.asserts package

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[List[AssertionDict] | None]

stderr: typing_extensions.NotRequired[List[AssertionDict] | None]

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[List[AssertionDict] | None]

command_version: typing_extensions.NotRequired[List[AssertionDict] | None]

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: int | None

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

inputs: Dict[str, Any]: Alias for field number 0

outputs: OutputsDict: Alias for field number 1

output_collections: Dict[str, Any]: Alias for field number 2

jobs: List[Dict[str, Any]]: Alias for field number 3

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

Bases: object

__init__(**kwds)[source]

cookies: RequestsCookieJar | None

api_key: str | None

keep_outputs_dir: str | None

property target_galaxy_version

property supports_test_data_download

get_tests_summary()[source]

get_tool_tests(tool_id: str, tool_version: str | None = None) → List[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: str, history_id: str | None = None, maxseconds=86400) → None[source]

wait_for(func: Callable, what: str = 'tool test run', **kwd) → None[source]

get_job_stdio(job_id: str) → Dict[str, Any][source]

get_history(history_name: str = 'test_history') → Dict[str, Any] | None[source]

test_history(require_new: bool = True, cleanup_callback: Callable[[str], None] | None = None) → Generator[str, None, None][source]

new_history(history_name: str = 'test_history', publish_history: bool = False) → str[source]

publish_history(history_id: str) → None[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: str | None = None) → Callable[[], None][source]

run_tool(testdef, history_id, resource_parameters=None) → RunToolResponse[source]

output_hid(output_data)[source]

delete_history(history: str) → None[source]

format_for_summary(blob, empty_message, prefix='| ')[source]

ensure_user_with_email(email, password=None)[source]

api_key_header(key: str | None, admin: bool, anon: bool, headers: Dict[str, str | None] | None) → Dict[str, str | None][source]

get_api_url(path: str) → str[source]

galaxy.tool_util.verify.interactor.prepare_request_params(data: Dict[str, Any] | None = None, files: Dict[str, Any] | None = None, as_json: bool = False, params: Dict[str, Any] | None = None, headers: Dict[str, str | None] | None = None, cookies: RequestsCookieJar | None = 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: str | None, hda_id: str, attributes: Dict[str, Any], test_data_downloader, dataset_fetcher=None, keep_outputs_dir: str | None = 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, **kwargs)[source]

Bases: Protocol

get_test_config(job_data: Dict[str, Any]) → Dict[str, Any] | None[source]

__init__(*args, **kwargs)

class galaxy.tool_util.verify.interactor.NullClientTestConfig(*args, **kwargs)[source]

Bases: TestConfig

get_test_config(job_data)[source]

class galaxy.tool_util.verify.interactor.DictClientTestConfig(tools)[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: Dict[str, Any] | None = None, register_job_data: Callable[[Dict[str, Any]], None] | None = None, test_index: int = 0, tool_version: str | None = None, quiet: bool = False, test_history: str | None = None, no_history_cleanup: bool = False, publish_history: bool = False, force_path_paste: bool = False, maxseconds: int = 86400, client_test_config: TestConfig | None = None, skip_with_reference_data: bool = False, skip_on_dynamic_param_errors: bool = False, _tool_test_dicts: List[ValidToolTestDict | InvalidToolTestDict] | None = 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.ToolTestDescriptionDict[source]

Bases: TypedDict

name: str

inputs: Any

outputs: Any

output_collections: List[Dict[str, Any]]

stdout: List[AssertionDict] | None

stderr: List[AssertionDict] | None

expect_exit_code: int | None

expect_failure: bool

expect_test_failure: bool

num_outputs: int | None

command_line: List[AssertionDict] | None

command_version: List[AssertionDict] | None

required_files: List[Any]

required_data_tables: List[Any]

required_loc_files: List[str]

error: bool

tool_id: str

tool_version: str | None

test_index: int

exception: str | None

class galaxy.tool_util.verify.interactor.ToolTestDescription(processed_test_dict: 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: ValidToolTestDict | InvalidToolTestDict)[source]

name: str

required_files: List[Any]

required_data_tables: List[Any]

required_loc_files: List[str]

num_outputs: int | None

exception: str | None

command_line: List[AssertionDict] | None

command_version: List[AssertionDict] | None

stdout: List[AssertionDict] | None

stderr: List[AssertionDict] | None

expect_exit_code: int | None

expect_failure: bool

expect_test_failure: bool

test_data()[source]: Iterator over metadata representing the required files for upload.

to_dict() → ToolTestDescriptionDict[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

tool_id: str: Alias for field number 0

tool_version: str | None: Alias for field number 1

test_index: int: Alias for field number 2

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

Bases: tuple

tool_id: str: Alias for field number 0

exception: Exception: Alias for field number 1

was_recorded: bool: Alias for field number 2

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

Bases: object

__init__(default_suitename: str, test_json: str, append: bool = False, galaxy_url: str | None = 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: Logger | None = None, parallel_tests: int = 1, history_per_test_case: bool = False, history_name: str | None = None, no_history_reuse: bool = False, no_history_cleanup: bool = False, publish_history: bool = False, retries: int = 0, verify_kwds: Dict[str, Any] | None = 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: str | None = None, test_index: int = -1, page_size: int = 0, page_number: int = 0, test_filters: List[Callable[[TestReference], bool]] | None = None, log: Logger | None = 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: List[Callable[[TestReference], bool]] | None = None, log: Logger | None = None) → None[source]

galaxy.tool_util.verify.script.setup_global_logger(name: str, log_file: str | None = 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 53', 'STATS_BLT': 'true', 'GITHUB_REF_NAME': 'dev', 'ACCEPT_EULA': 'Y', 'DOTNET_SKIP_FIRST_TIME_EXPERIENCE': '1', 'GITHUB_ENV': '/home/runner/work/_temp/_runner_file_commands/set_env_b018a09b-0a17-4f35-be54-65638c09e206', 'STATS_RDCL': 'true', 'GITHUB_REPOSITORY_ID': '31211061', 'RUNNER_TRACKING_ID': 'github_ec7b73ec-2e31-4e08-a359-bfb4304395b8', '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': 'd02ac224290bb5db3f7fb496c155ac1feabd3328', '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/3.8.18/x64/lib/pkgconfig', 'Python2_ROOT_DIR': '/opt/hostedtoolcache/Python/3.8.18/x64', 'GITHUB_SHA': 'd02ac224290bb5db3f7fb496c155ac1feabd3328', 'ANDROID_NDK_HOME': '/usr/local/lib/android/sdk/ndk/25.2.9519653', 'GITHUB_ACTOR_ID': '46503462', 'POWERSHELL_DISTRIBUTION_CHANNEL': 'GitHub-Actions-ubuntu22', 'SELENIUM_JAR_PATH': '/usr/share/java/selenium-server.jar', 'GOROOT_1_21_X64': '/opt/hostedtoolcache/go/1.21.9/x64', 'pythonLocation': '/opt/hostedtoolcache/Python/3.8.18/x64', 'MFLAGS': '-w', 'ANDROID_NDK_LATEST_HOME': '/usr/local/lib/android/sdk/ndk/26.3.11579264', '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': 'davelopez', 'DOTNET_NOLOGO': '1', 'DOTNET_MULTILEVEL_LOOKUP': '0', 'JAVA_HOME_11_X64': '/usr/lib/jvm/temurin-11-jdk-amd64', 'GITHUB_REF': 'refs/heads/dev', 'GITHUB_RUN_NUMBER': '22087', 'Python3_ROOT_DIR': '/opt/hostedtoolcache/Python/3.8.18/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/3.8.18/x64/lib/python3.8/site-packages/pylibmagic:/opt/hostedtoolcache/Python/3.8.18/x64/lib', 'GITHUB_STATE': '/home/runner/work/_temp/_runner_file_commands/save_state_b018a09b-0a17-4f35-be54-65638c09e206', 'SHLVL': '1', 'ANDROID_NDK': '/usr/local/lib/android/sdk/ndk/25.2.9519653', 'ImageVersion': '20240414.1.0', 'PATH': '/opt/hostedtoolcache/Python/3.8.18/x64/bin:/opt/hostedtoolcache/Python/3.8.18/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-8.7', 'GITHUB_RETENTION_DAYS': '90', 'INVOCATION_ID': 'a30f4bc04a654477942397958b28c10e', 'XDG_CONFIG_HOME': '/home/runner/.config', 'GITHUB_ACTIONS': 'true', 'GITHUB_WORKFLOW_REF': 'galaxyproject/galaxy/.github/workflows/docs.yaml@refs/heads/dev', 'CONDA': '/usr/share/miniconda', 'GITHUB_HEAD_REF': '', 'STATS_EXTP': 'https://provjobdsettingscdn.blob.core.windows.net/settings/provjobdsettings-0.5.172+1/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': '590', '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_b018a09b-0a17-4f35-be54-65638c09e206', 'RUNNER_ARCH': 'X64', 'GITHUB_PATH': '/home/runner/work/_temp/_runner_file_commands/add_path_b018a09b-0a17-4f35-be54-65638c09e206', 'RUNNER_TOOL_CACHE': '/opt/hostedtoolcache', '_': '/usr/bin/make', 'ANDROID_NDK_ROOT': '/usr/local/lib/android/sdk/ndk/25.2.9519653', 'XDG_RUNTIME_DIR': '/run/user/1001', 'AGENT_TOOLSDIRECTORY': '/opt/hostedtoolcache', 'GITHUB_REPOSITORY': 'galaxyproject/galaxy', 'VCPKG_INSTALLATION_ROOT': '/usr/local/share/vcpkg', 'JOURNAL_STREAM': '8:20704', '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': '8796633264', 'HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS': '3650', 'GITHUB_ACTOR': 'davelopez', 'ANT_HOME': '/usr/share/ant', 'ImageOS': 'ubuntu22', 'Python_ROOT_DIR': '/opt/hostedtoolcache/Python/3.8.18/x64', 'ACTIONS_RUNNER_ACTION_ARCHIVE_CACHE': '/opt/actionarchivecache', 'TARGET_BRANCH': 'dev', 'GITHUB_OUTPUT': '/home/runner/work/_temp/_runner_file_commands/set_output_b018a09b-0a17-4f35-be54-65638c09e206', 'GITHUB_BASE_REF': '', 'STATS_V3PS': 'true', 'GITHUB_REPOSITORY_OWNER_ID': '7937847', 'GOROOT_1_22_X64': '/opt/hostedtoolcache/go/1.22.2/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/3.8.18/x64/lib/python3.8/site-packages/pylibmagic:', 'MAGIC': '/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/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 53', 'STATS_BLT': 'true', 'GITHUB_REF_NAME': 'dev', 'ACCEPT_EULA': 'Y', 'DOTNET_SKIP_FIRST_TIME_EXPERIENCE': '1', 'GITHUB_ENV': '/home/runner/work/_temp/_runner_file_commands/set_env_b018a09b-0a17-4f35-be54-65638c09e206', 'STATS_RDCL': 'true', 'GITHUB_REPOSITORY_ID': '31211061', 'RUNNER_TRACKING_ID': 'github_ec7b73ec-2e31-4e08-a359-bfb4304395b8', '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': 'd02ac224290bb5db3f7fb496c155ac1feabd3328', '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/3.8.18/x64/lib/pkgconfig', 'Python2_ROOT_DIR': '/opt/hostedtoolcache/Python/3.8.18/x64', 'GITHUB_SHA': 'd02ac224290bb5db3f7fb496c155ac1feabd3328', 'ANDROID_NDK_HOME': '/usr/local/lib/android/sdk/ndk/25.2.9519653', 'GITHUB_ACTOR_ID': '46503462', 'POWERSHELL_DISTRIBUTION_CHANNEL': 'GitHub-Actions-ubuntu22', 'SELENIUM_JAR_PATH': '/usr/share/java/selenium-server.jar', 'GOROOT_1_21_X64': '/opt/hostedtoolcache/go/1.21.9/x64', 'pythonLocation': '/opt/hostedtoolcache/Python/3.8.18/x64', 'MFLAGS': '-w', 'ANDROID_NDK_LATEST_HOME': '/usr/local/lib/android/sdk/ndk/26.3.11579264', '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': 'davelopez', 'DOTNET_NOLOGO': '1', 'DOTNET_MULTILEVEL_LOOKUP': '0', 'JAVA_HOME_11_X64': '/usr/lib/jvm/temurin-11-jdk-amd64', 'GITHUB_REF': 'refs/heads/dev', 'GITHUB_RUN_NUMBER': '22087', 'Python3_ROOT_DIR': '/opt/hostedtoolcache/Python/3.8.18/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/3.8.18/x64/lib/python3.8/site-packages/pylibmagic:/opt/hostedtoolcache/Python/3.8.18/x64/lib', 'GITHUB_STATE': '/home/runner/work/_temp/_runner_file_commands/save_state_b018a09b-0a17-4f35-be54-65638c09e206', 'SHLVL': '1', 'ANDROID_NDK': '/usr/local/lib/android/sdk/ndk/25.2.9519653', 'ImageVersion': '20240414.1.0', 'PATH': '/opt/hostedtoolcache/Python/3.8.18/x64/bin:/opt/hostedtoolcache/Python/3.8.18/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-8.7', 'GITHUB_RETENTION_DAYS': '90', 'INVOCATION_ID': 'a30f4bc04a654477942397958b28c10e', 'XDG_CONFIG_HOME': '/home/runner/.config', 'GITHUB_ACTIONS': 'true', 'GITHUB_WORKFLOW_REF': 'galaxyproject/galaxy/.github/workflows/docs.yaml@refs/heads/dev', 'CONDA': '/usr/share/miniconda', 'GITHUB_HEAD_REF': '', 'STATS_EXTP': 'https://provjobdsettingscdn.blob.core.windows.net/settings/provjobdsettings-0.5.172+1/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': '590', '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_b018a09b-0a17-4f35-be54-65638c09e206', 'RUNNER_ARCH': 'X64', 'GITHUB_PATH': '/home/runner/work/_temp/_runner_file_commands/add_path_b018a09b-0a17-4f35-be54-65638c09e206', 'RUNNER_TOOL_CACHE': '/opt/hostedtoolcache', '_': '/usr/bin/make', 'ANDROID_NDK_ROOT': '/usr/local/lib/android/sdk/ndk/25.2.9519653', 'XDG_RUNTIME_DIR': '/run/user/1001', 'AGENT_TOOLSDIRECTORY': '/opt/hostedtoolcache', 'GITHUB_REPOSITORY': 'galaxyproject/galaxy', 'VCPKG_INSTALLATION_ROOT': '/usr/local/share/vcpkg', 'JOURNAL_STREAM': '8:20704', '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': '8796633264', 'HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS': '3650', 'GITHUB_ACTOR': 'davelopez', 'ANT_HOME': '/usr/share/ant', 'ImageOS': 'ubuntu22', 'Python_ROOT_DIR': '/opt/hostedtoolcache/Python/3.8.18/x64', 'ACTIONS_RUNNER_ACTION_ARCHIVE_CACHE': '/opt/actionarchivecache', 'TARGET_BRANCH': 'dev', 'GITHUB_OUTPUT': '/home/runner/work/_temp/_runner_file_commands/set_output_b018a09b-0a17-4f35-be54-65638c09e206', 'GITHUB_BASE_REF': '', 'STATS_V3PS': 'true', 'GITHUB_REPOSITORY_OWNER_ID': '7937847', 'GOROOT_1_22_X64': '/opt/hostedtoolcache/go/1.22.2/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/3.8.18/x64/lib/python3.8/site-packages/pylibmagic:', 'MAGIC': '/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/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: int | float, delta: int | float = 0.25, polling_backoff: int | float = 0, sleep_: Callable | None = 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]