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galaxy_test.base package

Submodules

galaxy_test.base.api module

class galaxy_test.base.api.UsesApiTestCaseMixin

Bases: object

tearDown()

class galaxy_test.base.api.ApiTestInteractor(test_case, api_key=None)

Bases: galaxy_test.base.interactor.TestCaseGalaxyInteractor

Specialized variant of the API interactor (originally developed for tool functional tests) for testing the API generally.

__init__(test_case, api_key=None)

Initialize self. See help(type(self)) for accurate signature.

get(*args, **kwds)

post(*args, **kwds)

delete(*args, **kwds)

patch(*args, **kwds)

put(*args, **kwds)

galaxy_test.base.api_asserts module

Utility methods for making assertions about Galaxy API responses, etc…

galaxy_test.base.api_asserts.assert_status_code_is(response: requests.models.Response, expected_status_code: int)

Assert that the supplied response has the expect status code.

galaxy_test.base.api_asserts.assert_status_code_is_ok(response: requests.models.Response)

Assert that the supplied response is okay.

The easier alternative response.raise_for_status() might be perferable generally.

See also

requests.Response.raise_for_status()

galaxy_test.base.api_asserts.assert_has_keys(response: dict, *keys: str)

Assert that the supplied response (dict) has the supplied keys.

galaxy_test.base.api_asserts.assert_not_has_keys(response: dict, *keys: str)

Assert that the supplied response (dict) does not have the supplied keys.

galaxy_test.base.api_asserts.assert_error_code_is(response: Union[requests.models.Response, dict], error_code: int)

Assert that the supplied response has the supplied Galaxy error code.

Galaxy error codes can be imported from galaxy.exceptions.error_codes to test against.

from galaxy.exceptions import error_codes
assert_error_code_is(response, error_codes.USER_REQUEST_MISSING_PARAMETER)

galaxy_test.base.api_asserts.assert_object_id_error(response: requests.models.Response)

galaxy_test.base.api_asserts.assert_error_message_contains(response: Union[requests.models.Response, dict], expected_contains: str)

galaxy_test.base.api_asserts.assert_has_key(response: dict, *keys: str)

Assert that the supplied response (dict) has the supplied keys.

galaxy_test.base.api_util module

galaxy_test.base.api_util.get_admin_api_key() → str

Test admin API key to use for functional tests.

This key should be configured as a admin API key and should be able to create additional users and keys.

galaxy_test.base.api_util.get_user_api_key() → Optional[str]

Test user API key to use for functional tests.

If set, this should drive API based testing - if not set an admin API key will be used to create a new user and API key for tests.

galaxy_test.base.constants module

Just constants useful for testing across test types.

galaxy_test.base.env module

Base utilities for working Galaxy test environments.

galaxy_test.base.env.setup_keep_outdir() → str

galaxy_test.base.env.target_url_parts() → Tuple[str, Optional[str], str]

galaxy_test.base.env.get_ip_address(ifname: str) → str

galaxy_test.base.instrument module

Utilities to help instrument tool tests.

Including structured data nose plugin that allows storing arbitrary structured data on a per test case basis - used by tool test to store inputs, output problems, job tests, etc… but could easily by used by other test types in a different way.

galaxy_test.base.instrument.register_job_data(data)

galaxy_test.base.instrument.fetch_job_data()

class galaxy_test.base.instrument.StructuredTestDataPlugin

Bases: nose.plugins.base.Plugin

name = 'structureddata'

options(parser, env)

Register commandline options.

Implement this method for normal options behavior with protection from OptionConflictErrors. If you override this method and want the default –with-$name option to be registered, be sure to call super().

configure(options, conf)

Configure the plugin and system, based on selected options.

The base plugin class sets the plugin to enabled if the enable option for the plugin (self.enableOpt) is true.

finalize(result)

addError(test, *args, **kwds)

addFailure(test, *args, **kwds)

addSuccess(test, *args, **kwds)

report(stream)

galaxy_test.base.interactor module

class galaxy_test.base.interactor.TestCaseGalaxyInteractor(functional_test_case, test_user=None, api_key=None)

Bases: galaxy.tool_util.verify.interactor.GalaxyInteractorApi

__init__(functional_test_case, test_user=None, api_key=None)

Initialize self. See help(type(self)) for accurate signature.

galaxy_test.base.nose_util module

Utilities for dealing with nose.

There was some duplication between Galaxy, Tool Shed, and Install/Test, trying to reduce that here.

galaxy_test.base.nose_util.run(test_config, plugins=None)

galaxy_test.base.populators module

Abstractions used by the Galaxy testing frameworks for interacting with the Galaxy API.

These abstractions are geared toward testing use cases and populating fixtures. For a more general framework for working with the Galaxy API checkout bioblend.

The populators are broken into different categories of data one might want to populate and work with (datasets, histories, libraries, and workflows). Within each populator type abstract classes describe high-level functionality that depend on abstract HTTP verbs executions (e.g. methods for executing GET, POST, DELETE). The abstract classes are galaxy_test.base.populators.BaseDatasetPopulator, galaxy_test.base.populators.BaseWorkflowPopulator, and galaxy_test.base.populators.BaseDatasetCollectionPopulator.

There are a few different concrete ways to supply these low-level verb executions. For instance galaxy_test.base.populators.DatasetPopulator implements the abstract galaxy_test.base.populators.BaseDatasetPopulator by leveraging a galaxy interactor galaxy.tool_util.interactor.GalaxyInteractorApi. It is non-intuitive that the Galaxy testing framework uses the tool testing code inside Galaxy’s code base for a lot of heavy lifting. This is due to the API testing framework organically growing from the tool testing framework that predated it and then the tool testing framework being extracted for re-use in Planemo, etc..

These other two concrete implementation of the populators are much more direct and intuitive. galaxy_test.base.populators.GiDatasetPopulator, et. al. are populators built based on Bioblend gi objects to build URLs and describe API keys. galaxy_test.selenium.framework.SeleniumSessionDatasetPopulator, et al. are populators built based on Selenium sessions to leverage Galaxy cookies for auth for instance.

All three of these implementations are now effectively light wrappers around requests. Not leveraging requests directly is a bit ugly and this ugliness again stems from these organically growing from a framework that originally didn’t use requests at all.

API tests and Selenium tests routinely use requests directly and that is totally fine, requests should just be filtered through the verb abstractions if that functionality is then added to populators to be shared across tests or across testing frameworks.

galaxy_test.base.populators.flakey(method)

galaxy_test.base.populators.skip_without_tool(tool_id)

Decorate an API test method as requiring a specific tool.

Have test framework skip the test case if the tool is unavailable.

galaxy_test.base.populators.skip_without_datatype(extension)

Decorate an API test method as requiring a specific datatype.

Have test framework skip the test case if the datatype is unavailable.

galaxy_test.base.populators.is_site_up(url)

galaxy_test.base.populators.skip_if_site_down(url)

galaxy_test.base.populators.skip_if_toolshed_down(method)

galaxy_test.base.populators.skip_if_github_down(method)

galaxy_test.base.populators.summarize_instance_history_on_error(method)

galaxy_test.base.populators.uses_test_history(**test_history_kwd)

Can override require_new and cancel_executions using kwds to decorator.

class galaxy_test.base.populators.BasePopulator

Bases: object

class galaxy_test.base.populators.BaseDatasetPopulator

Bases: galaxy_test.base.populators.BasePopulator

Abstract description of API operations optimized for testing Galaxy - implementations must implement _get, _post and _delete.

new_dataset(history_id: str, content=None, wait: bool = False, **kwds) → str

Create a new history dataset instance (HDA) and return its ID.

Returns

the HDA id of the new object

new_dataset_request(history_id: str, content=None, wait: bool = False, **kwds) → requests.models.Response

Lower-level dataset creation that returns the upload tool response object.

fetch(payload: dict, assert_ok: bool = True, timeout: Union[int, float] = 60, wait: Optional[bool] = None)

wait_for_tool_run(history_id: str, run_response: requests.models.Response, timeout: Union[int, float] = 60, assert_ok: bool = True)

check_run(run_response: requests.models.Response) → dict

wait_for_history(history_id: str, assert_ok: bool = False, timeout: Union[int, float] = 60) → str

wait_for_history_jobs(history_id: str, assert_ok: bool = False, timeout: Union[int, float] = 60)

wait_for_job(job_id: str, assert_ok: bool = False, timeout: Union[int, float] = 60)

get_job_details(job_id: str, full: bool = False) → requests.models.Response

cancel_history_jobs(history_id: str, wait=True) → None

history_jobs(history_id: str) → dict

active_history_jobs(history_id: str) → list

cancel_job(job_id: str) → requests.models.Response

delete_history(history_id: str) → None

delete_dataset(history_id: str, content_id: str) → requests.models.Response

create_tool_from_path(tool_path: str) → requests.models.Response

create_tool(representation, tool_directory: Optional[str] = None) → requests.models.Response

list_dynamic_tools() → list

show_dynamic_tool(uuid) → dict

deactivate_dynamic_tool(uuid) → dict

test_history(cancel_executions: bool = True, require_new: bool = True, **kwds)

new_history(name='API Test History', **kwds) → str

upload_payload(history_id: str, content: Optional[str] = None, **kwds) → dict

get_remote_files(target: str = 'ftp') → dict

run_tool_payload(tool_id: str, inputs: dict, history_id: str, **kwds) → dict

build_tool_state(tool_id: str, history_id: str)

run_tool(tool_id: str, inputs: dict, history_id: str, assert_ok: bool = True, **kwds)

tools_post(payload: dict, url='tools') → requests.models.Response

get_history_dataset_content(history_id: str, wait=True, filename=None, type='text', raw=False, **kwds)

get_history_dataset_details(history_id: str, **kwds) → dict

get_history_dataset_details_raw(history_id: str, dataset_id: str) → requests.models.Response

get_history_dataset_extra_files(history_id: str, **kwds) → list

get_history_collection_details(history_id: str, **kwds) → dict

run_collection_creates_list(history_id: str, hdca_id: str) → requests.models.Response

run_exit_code_from_file(history_id: str, hdca_id: str) → dict

ds_entry(history_content: dict) → dict

dataset_storage_info(dataset_id: str) → dict

get_roles() → list

user_email() → str

user_id() → str

user_private_role_id() → str

create_role(user_ids: list, description: Optional[str] = None) → dict

create_quota(quota_payload: dict) → dict

get_quotas() → list

make_private(history_id: str, dataset_id: str) → dict

validate_dataset(history_id, dataset_id)

validate_dataset_and_wait(history_id, dataset_id)

setup_history_for_export_testing(history_name)

prepare_export(history_id, data)

export_url(history_id, data, check_download=True)

get_export_url(export_url)

import_history(import_data)

import_history_and_wait_for_name(import_data, history_name)

rename_history(history_id, new_name)

get_histories()

wait_on_history_length(history_id, wait_on_history_length)

history_length(history_id)

reimport_history(history_id, history_name, wait_on_history_length, export_kwds, url, api_key)

get_random_name(prefix=None, suffix=None, len=10)

wait_for_dataset(history_id, dataset_id, assert_ok=False, timeout=60)

class galaxy_test.base.populators.GalaxyInteractorHttpMixin

Bases: object

galaxy_interactor: galaxy_test.base.api.ApiTestInteractor

class galaxy_test.base.populators.DatasetPopulator(galaxy_interactor)

Bases: galaxy_test.base.populators.GalaxyInteractorHttpMixin, galaxy_test.base.populators.BaseDatasetPopulator

__init__(galaxy_interactor)

Initialize self. See help(type(self)) for accurate signature.

galaxy_interactor: galaxy_test.base.api.ApiTestInteractor

class galaxy_test.base.populators.BaseWorkflowPopulator

Bases: galaxy_test.base.populators.BasePopulator

load_workflow(name: str, content: str = '{\n    "a_galaxy_workflow": "true", \n    "annotation": "simple workflow",\n    "format-version": "0.1", \n    "name": "TestWorkflow1", \n    "steps": {\n        "0": {\n            "annotation": "input1 description", \n            "id": 0, \n            "input_connections": {}, \n            "inputs": [\n                {\n                    "description": "input1 description", \n                    "name": "WorkflowInput1"\n                }\n            ], \n            "name": "Input dataset", \n            "outputs": [], \n            "position": {\n                "left": 199.55555772781372, \n                "top": 200.66666460037231\n            }, \n            "tool_errors": null, \n            "tool_id": null, \n            "tool_state": "{\\"name\\": \\"WorkflowInput1\\"}", \n            "tool_version": null, \n            "type": "data_input", \n            "user_outputs": []\n        }, \n        "1": {\n            "annotation": "", \n            "id": 1, \n            "input_connections": {}, \n            "inputs": [\n                {\n                    "description": "", \n                    "name": "WorkflowInput2"\n                }\n            ], \n            "name": "Input dataset", \n            "outputs": [], \n            "position": {\n                "left": 206.22221422195435, \n                "top": 327.33335161209106\n            }, \n            "tool_errors": null, \n            "tool_id": null, \n            "tool_state": "{\\"name\\": \\"WorkflowInput2\\"}", \n            "tool_version": null, \n            "type": "data_input", \n            "user_outputs": []\n        }, \n        "2": {\n            "annotation": "", \n            "id": 2, \n            "input_connections": {\n                "input1": {\n                    "id": 0, \n                    "output_name": "output"\n                }, \n                "queries_0|input2": {\n                    "id": 1, \n                    "output_name": "output"\n                }\n            }, \n            "inputs": [], \n            "name": "Concatenate datasets", \n            "outputs": [\n                {\n                    "name": "out_file1", \n                    "type": "input"\n                }\n            ], \n            "position": {\n                "left": 419.33335876464844, \n                "top": 200.44446563720703\n            }, \n            "post_job_actions": {}, \n            "tool_errors": null, \n            "tool_id": "cat1", \n            "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input1\\": \\"null\\", \\"queries\\": \\"[{\\\\\\"input2\\\\\\": null, \\\\\\"__index__\\\\\\": 0}]\\"}", \n            "tool_version": "1.0.0", \n            "type": "tool", \n            "user_outputs": []\n        }\n    }\n}\n', add_pja=False) → dict

load_random_x2_workflow(name: str) → dict

load_workflow_from_resource(name: str, filename: Optional[str] = None) → dict

simple_workflow(name: str, **create_kwds) → str

import_workflow_from_path(from_path: str) → str

create_workflow(workflow: dict, **create_kwds) → str

create_workflow_response(workflow: dict, **create_kwds) → requests.models.Response

upload_yaml_workflow(has_yaml, **kwds) → str

wait_for_invocation(workflow_id: str, invocation_id: str, timeout: Union[int, float] = 60, assert_ok: bool = True)

history_invocations(history_id: str) → list

wait_for_history_workflows(history_id, assert_ok=True, timeout=60, expected_invocation_count=None)

wait_for_workflow(workflow_id, invocation_id, history_id, assert_ok=True, timeout=60)

Wait for a workflow invocation to completely schedule and then history to be complete.

get_invocation(invocation_id)

get_biocompute_object(invocation_id)

validate_biocompute_object(bco, expected_schema_version='https://w3id.org/ieee/ieee-2791-schema/2791object.json')

invoke_workflow_raw(workflow_id, request: dict) → requests.models.Response

invoke_workflow(history_id: str, workflow_id: str, inputs: Optional[dict] = None, request: Optional[dict] = None, assert_ok: bool = True)

workflow_report_json(workflow_id: str, invocation_id: str) → dict

download_workflow(workflow_id: str, style: Optional[str] = None, history_id: Optional[str] = None) → dict

update_workflow(workflow_id: str, workflow_object: dict) → requests.models.Response

refactor_workflow(workflow_id: str, actions: list, dry_run: Optional[bool] = None, style: Optional[str] = None) → requests.models.Response

export_for_update(workflow_id)

run_workflow(has_workflow, test_data=None, history_id=None, wait=True, source_type=None, jobs_descriptions=None, expected_response=200, assert_ok=True, client_convert=None, round_trip_format_conversion=False, raw_yaml=False)

High-level wrapper around workflow API, etc. to invoke format 2 workflows.

dump_workflow(workflow_id, style=None)

class galaxy_test.base.populators.RunJobsSummary(history_id, workflow_id, invocation_id, inputs, jobs, invocation, workflow_request)

Bases: tuple

property history_id

Alias for field number 0

property inputs

Alias for field number 3

property invocation

Alias for field number 5

property invocation_id

Alias for field number 2

property jobs

Alias for field number 4

property workflow_id

Alias for field number 1

property workflow_request

Alias for field number 6

class galaxy_test.base.populators.WorkflowPopulator(galaxy_interactor)

Bases: galaxy_test.base.populators.GalaxyInteractorHttpMixin, galaxy_test.base.populators.BaseWorkflowPopulator, gxformat2.interface.ImporterGalaxyInterface

__init__(galaxy_interactor)

Initialize self. See help(type(self)) for accurate signature.

galaxy_interactor: galaxy_test.base.api.ApiTestInteractor

import_workflow(workflow, **kwds)

Import a workflow via POST /api/workflows or comparable interface into Galaxy.

import_tool(tool)

Import a workflow via POST /api/workflows or comparable interface into Galaxy.

scaling_workflow_yaml(**kwd)

class galaxy_test.base.populators.LibraryPopulator(galaxy_interactor)

Bases: object

__init__(galaxy_interactor)

Initialize self. See help(type(self)) for accurate signature.

get_libraries()

new_private_library(name)

new_library(name)

set_permissions(library_id, role_id=None)

user_email()

user_private_role_id()

create_dataset_request(library, **kwds)

new_library_dataset(name, **create_dataset_kwds)

wait_on_library_dataset(library_id, dataset_id)

raw_library_contents_create(library_id, payload, files=None)

show_ld(library_id, library_dataset_id)

show_ldda(ldda_id)

new_library_dataset_in_private_library(library_name='private_dataset', wait=True)

get_library_contents_with_path(library_id, path)

setup_fetch_to_folder(test_name)

class galaxy_test.base.populators.BaseDatasetCollectionPopulator

Bases: object

create_list_from_pairs(history_id, pairs, name='Dataset Collection from pairs')

nested_collection_identifiers(history_id, collection_type)

create_nested_collection(history_id, collection_type, name=None, collection=None, element_identifiers=None)

Create a nested collection either from collection or using collection_type).

create_list_of_pairs_in_history(history_id, **kwds)

create_list_of_list_in_history(history_id, **kwds)

create_pair_in_history(history_id, **kwds)

create_list_in_history(history_id, **kwds)

upload_collection(history_id, collection_type, elements, **kwds)

create_list_payload(history_id, **kwds)

create_pair_payload(history_id, **kwds)

wait_for_fetched_collection(fetch_response)

pair_identifiers(history_id, contents=None)

list_identifiers(history_id, contents=None)

wait_for_dataset_collection(create_payload, assert_ok=False, timeout=60)

class galaxy_test.base.populators.DatasetCollectionPopulator(galaxy_interactor: galaxy_test.base.api.ApiTestInteractor)

Bases: galaxy_test.base.populators.BaseDatasetCollectionPopulator

__init__(galaxy_interactor: galaxy_test.base.api.ApiTestInteractor)

Initialize self. See help(type(self)) for accurate signature.

galaxy_test.base.populators.load_data_dict(history_id, test_data, dataset_populator, dataset_collection_populator)

Load a dictionary as inputs to a workflow (test data focused).

galaxy_test.base.populators.stage_inputs(galaxy_interactor, history_id, job, use_path_paste=True, use_fetch_api=True, to_posix_lines=True)

Alternative to load_data_dict that uses production-style workflow inputs.

galaxy_test.base.populators.stage_rules_example(galaxy_interactor, history_id, example)

Wrapper around stage_inputs for staging collections defined by rules spec DSL.

galaxy_test.base.populators.wait_on_state(state_func: Callable, desc='state', skip_states=None, ok_states=None, assert_ok=False, timeout=60) → str

class galaxy_test.base.populators.GiHttpMixin

Bases: object

Mixin for adapting Galaxy testing populators helpers to bioblend.

class galaxy_test.base.populators.GiDatasetPopulator(gi)

Bases: galaxy_test.base.populators.BaseDatasetPopulator, galaxy_test.base.populators.GiHttpMixin

Implementation of BaseDatasetPopulator backed by bioblend.

__init__(gi)

Construct a dataset populator from a bioblend GalaxyInstance.

class galaxy_test.base.populators.GiDatasetCollectionPopulator(gi)

Bases: galaxy_test.base.populators.BaseDatasetCollectionPopulator, galaxy_test.base.populators.GiHttpMixin

Implementation of BaseDatasetCollectionPopulator backed by bioblend.

__init__(gi)

Construct a dataset collection populator from a bioblend GalaxyInstance.

class galaxy_test.base.populators.GiWorkflowPopulator(gi)

Bases: galaxy_test.base.populators.BaseWorkflowPopulator, galaxy_test.base.populators.GiHttpMixin

Implementation of BaseWorkflowPopulator backed by bioblend.

__init__(gi)

Construct a workflow populator from a bioblend GalaxyInstance.

galaxy_test.base.populators.wait_on(function, desc, timeout=60)

galaxy_test.base.rules_test_data module

galaxy_test.base.rules_test_data.check_example_1(hdca, dataset_populator)

galaxy_test.base.rules_test_data.check_example_2(hdca, dataset_populator)

galaxy_test.base.rules_test_data.check_example_3(hdca, dataset_populator)

galaxy_test.base.rules_test_data.check_example_4(hdca, dataset_populator)

galaxy_test.base.rules_test_data.check_example_5(hdca, dataset_populator)

galaxy_test.base.rules_test_data.check_example_6(hdca, dataset_populator)

galaxy_test.base.ssh_util module

galaxy_test.base.ssh_util.generate_ssh_keys()

Returns a named tuple with private and public key and their paths.

galaxy_test.base.testcase module

class galaxy_test.base.testcase.FunctionalTestCase(methodName='runTest')

Bases: unittest.case.TestCase

Base class for tests targetting actual Galaxy servers.

Subclass should override galaxy_driver_class if a Galaxy server needs to be launched to run the test, this base class assumes a server is already running.

galaxy_driver_class: Optional[type] = None

history_id: Optional[str]

host: str

port: Optional[str]

url: str

keepOutdir: str

test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver

setUp() → None

Hook method for setting up the test fixture before exercising it.

classmethod setUpClass()

Configure and start Galaxy for a test.

classmethod tearDownClass()

Shutdown Galaxy server and cleanup temp directory.

get_filename(filename: str) → str

galaxy_test.base.workflow_fixtures module