toil.test.server.serverTest

Module Contents

Classes

ToilServerUtilsTest	Tests for the utility functions used by the Toil server.
hidden
FileStateStoreTest	Test file-based state storage.
FileStateStoreURLTest	Test file-based state storage using URLs instead of local paths.
BucketUsingTest	Base class for tests that need a bucket.
AWSStateStoreTest	Test AWS-based state storage.
AbstractToilWESServerTest	Class for server tests that provides a self.app in testing mode.
ToilWESServerBenchTest	Tests for Toil's Workflow Execution Service API that don't run workflows.
ToilWESServerWorkflowTest	Tests of the WES server running workflows.
ToilWESServerCeleryWorkflowTest	End-to-end workflow-running tests against Celery.
ToilWESServerCeleryS3StateWorkflowTest	Test the server with Celery and state stored in S3.

Attributes

logger

toil.test.server.serverTest.logger

class toil.test.server.serverTest.ToilServerUtilsTest(methodName='runTest')

Bases: toil.test.ToilTest

digraph inheritanceeeacb90502 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; "ToilServerUtilsTest" [URL="#toil.test.server.serverTest.ToilServerUtilsTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Tests for the utility functions used by the Toil server."]; "ToilTest" -> "ToilServerUtilsTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "ToilTest" [URL="../../index.html#toil.test.ToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A common base class for Toil tests."]; "TestCase" -> "ToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

Tests for the utility functions used by the Toil server.

test_workflow_canceling_recovery()

Make sure that a workflow in CANCELING state will be recovered to a terminal state eventually even if the workflow runner Celery task goes away without flipping the state.

class toil.test.server.serverTest.hidden

class AbstractStateStoreTest(methodName='runTest')

Bases: toil.test.ToilTest

digraph inheritance5060f800d4 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "AbstractStateStoreTest" [URL="#toil.test.server.serverTest.hidden.AbstractStateStoreTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Basic tests for state stores."]; "ToilTest" -> "AbstractStateStoreTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; "ToilTest" [URL="../../index.html#toil.test.ToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A common base class for Toil tests."]; "TestCase" -> "ToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

Basic tests for state stores.

abstract get_state_store()

Make a state store to test, on a single fixed URL.

Return type:

AbstractStateStore

test_state_store()

Make sure that the state store under test can store and load keys.

Return type:

None

class toil.test.server.serverTest.FileStateStoreTest(methodName='runTest')

Bases: hidden

digraph inheritance53ef2783ed { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "AbstractStateStoreTest" [URL="#toil.test.server.serverTest.hidden.AbstractStateStoreTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Basic tests for state stores."]; "ToilTest" -> "AbstractStateStoreTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "FileStateStoreTest" [URL="#toil.test.server.serverTest.FileStateStoreTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Test file-based state storage."]; "AbstractStateStoreTest" -> "FileStateStoreTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; "ToilTest" [URL="../../index.html#toil.test.ToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A common base class for Toil tests."]; "TestCase" -> "ToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

Test file-based state storage.

setUp()

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

Return type:

None

get_state_store()

Make a state store to test, on a single fixed local path.

Return type:

AbstractStateStore

class toil.test.server.serverTest.FileStateStoreURLTest(methodName='runTest')

Bases: hidden

digraph inheritance26f25b1a02 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "AbstractStateStoreTest" [URL="#toil.test.server.serverTest.hidden.AbstractStateStoreTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Basic tests for state stores."]; "ToilTest" -> "AbstractStateStoreTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "FileStateStoreURLTest" [URL="#toil.test.server.serverTest.FileStateStoreURLTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Test file-based state storage using URLs instead of local paths."]; "AbstractStateStoreTest" -> "FileStateStoreURLTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; "ToilTest" [URL="../../index.html#toil.test.ToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A common base class for Toil tests."]; "TestCase" -> "ToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

Test file-based state storage using URLs instead of local paths.

setUp()

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

Return type:

None

get_state_store()

Make a state store to test, on a single fixed URL.

Return type:

AbstractStateStore

class toil.test.server.serverTest.BucketUsingTest(methodName='runTest')

Bases: toil.test.ToilTest

digraph inheritance61fd6478b6 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "BucketUsingTest" [URL="#toil.test.server.serverTest.BucketUsingTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Base class for tests that need a bucket."]; "ToilTest" -> "BucketUsingTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; "ToilTest" [URL="../../index.html#toil.test.ToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A common base class for Toil tests."]; "TestCase" -> "ToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

Base class for tests that need a bucket.

region: str | None

s3_resource: mypy_boto3_s3.S3ServiceResource | None

bucket: mypy_boto3_s3.service_resource.Bucket | None

bucket_name: str | None

classmethod setUpClass()

Set up the class with a single pre-existing AWS bucket for all tests.

Return type:

None

classmethod tearDownClass()

Hook method for deconstructing the class fixture after running all tests in the class.

Return type:

None

class toil.test.server.serverTest.AWSStateStoreTest(methodName='runTest')

Bases: hidden, BucketUsingTest

digraph inheritancea11779b881 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "AWSStateStoreTest" [URL="#toil.test.server.serverTest.AWSStateStoreTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Test AWS-based state storage."]; "AbstractStateStoreTest" -> "AWSStateStoreTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "BucketUsingTest" -> "AWSStateStoreTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "AbstractStateStoreTest" [URL="#toil.test.server.serverTest.hidden.AbstractStateStoreTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Basic tests for state stores."]; "ToilTest" -> "AbstractStateStoreTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "BucketUsingTest" [URL="#toil.test.server.serverTest.BucketUsingTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Base class for tests that need a bucket."]; "ToilTest" -> "BucketUsingTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; "ToilTest" [URL="../../index.html#toil.test.ToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A common base class for Toil tests."]; "TestCase" -> "ToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

Test AWS-based state storage.

bucket_path = 'prefix/of/keys'

get_state_store()

Make a state store to test, on a single fixed URL.

Return type:

AbstractStateStore

test_state_store_paths()

Make sure that the S3 state store puts things in the right places.

We don’t really care about the exact internal structure, but we do care about actually being under the path we are supposed to use.

Return type:

None

class toil.test.server.serverTest.AbstractToilWESServerTest(*args, **kwargs)

Bases: toil.test.ToilTest

digraph inheritance994295b50d { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "AbstractToilWESServerTest" [URL="#toil.test.server.serverTest.AbstractToilWESServerTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Class for server tests that provides a self.app in testing mode."]; "ToilTest" -> "AbstractToilWESServerTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; "ToilTest" [URL="../../index.html#toil.test.ToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A common base class for Toil tests."]; "TestCase" -> "ToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

Class for server tests that provides a self.app in testing mode.

setUp()

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

Return type:

None

tearDown()

Hook method for deconstructing the test fixture after testing it.

Return type:

None

class toil.test.server.serverTest.ToilWESServerBenchTest(*args, **kwargs)

Bases: AbstractToilWESServerTest

digraph inheritance9a1150eb08 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "AbstractToilWESServerTest" [URL="#toil.test.server.serverTest.AbstractToilWESServerTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Class for server tests that provides a self.app in testing mode."]; "ToilTest" -> "AbstractToilWESServerTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; "ToilTest" [URL="../../index.html#toil.test.ToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A common base class for Toil tests."]; "TestCase" -> "ToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "ToilWESServerBenchTest" [URL="#toil.test.server.serverTest.ToilWESServerBenchTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Tests for Toil's Workflow Execution Service API that don't run workflows."]; "AbstractToilWESServerTest" -> "ToilWESServerBenchTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

Tests for Toil’s Workflow Execution Service API that don’t run workflows.

test_home()

Test the homepage endpoint.

Return type:

None

test_health()

Test the health check endpoint.

Return type:

None

test_get_service_info()

Test the GET /service-info endpoint.

Return type:

None

class toil.test.server.serverTest.ToilWESServerWorkflowTest(*args, **kwargs)

Bases: AbstractToilWESServerTest

digraph inheritance01c04fb999 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "AbstractToilWESServerTest" [URL="#toil.test.server.serverTest.AbstractToilWESServerTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Class for server tests that provides a self.app in testing mode."]; "ToilTest" -> "AbstractToilWESServerTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; "ToilTest" [URL="../../index.html#toil.test.ToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A common base class for Toil tests."]; "TestCase" -> "ToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "ToilWESServerWorkflowTest" [URL="#toil.test.server.serverTest.ToilWESServerWorkflowTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Tests of the WES server running workflows."]; "AbstractToilWESServerTest" -> "ToilWESServerWorkflowTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

Tests of the WES server running workflows.

run_zip_workflow(zip_path, include_message=True, include_params=True)

We have several zip file tests; this submits a zip file and makes sure it ran OK.

If include_message is set to False, don’t send a “message” argument in workflow_params. If include_params is also set to False, don’t send workflow_params at all.

Parameters:

• zip_path (str) –

• include_message (bool) –

• include_params (bool) –

Return type:

None

test_run_workflow_relative_url_no_attachments_fails()

Test run example CWL workflow from relative workflow URL but with no attachments.

Return type:

None

test_run_workflow_relative_url()

Test run example CWL workflow from relative workflow URL.

Return type:

None

test_run_workflow_https_url()

Test run example CWL workflow from the Internet.

Return type:

None

test_run_workflow_single_file_zip()

Test run example CWL workflow from single-file ZIP.

Return type:

None

test_run_workflow_multi_file_zip()

Test run example CWL workflow from multi-file ZIP.

Return type:

None

test_run_workflow_manifest_zip()

Test run example CWL workflow from ZIP with manifest.

Return type:

None

test_run_workflow_inputs_zip()

Test run example CWL workflow from ZIP without manifest but with inputs.

Return type:

None

test_run_workflow_manifest_and_inputs_zip()

Test run example CWL workflow from ZIP with manifest and inputs.

Return type:

None

test_run_workflow_no_params_zip()

Test run example CWL workflow from ZIP without workflow_params.

Return type:

None

test_run_and_cancel_workflows()

Run two workflows, cancel one of them, and make sure they all exist.

Return type:

None

class toil.test.server.serverTest.ToilWESServerCeleryWorkflowTest(*args, **kwargs)

Bases: ToilWESServerWorkflowTest

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End-to-end workflow-running tests against Celery.

class toil.test.server.serverTest.ToilWESServerCeleryS3StateWorkflowTest(*args, **kwargs)

Bases: ToilWESServerWorkflowTest, BucketUsingTest

digraph inheritance49302f0fbd { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "AbstractToilWESServerTest" [URL="#toil.test.server.serverTest.AbstractToilWESServerTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Class for server tests that provides a self.app in testing mode."]; "ToilTest" -> "AbstractToilWESServerTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "BucketUsingTest" [URL="#toil.test.server.serverTest.BucketUsingTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Base class for tests that need a bucket."]; "ToilTest" -> "BucketUsingTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "TestCase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A class whose instances are single test cases."]; "ToilTest" [URL="../../index.html#toil.test.ToilTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A common base class for Toil tests."]; "TestCase" -> "ToilTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "ToilWESServerCeleryS3StateWorkflowTest" [URL="#toil.test.server.serverTest.ToilWESServerCeleryS3StateWorkflowTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Test the server with Celery and state stored in S3."]; "ToilWESServerWorkflowTest" -> "ToilWESServerCeleryS3StateWorkflowTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "BucketUsingTest" -> "ToilWESServerCeleryS3StateWorkflowTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; "ToilWESServerWorkflowTest" [URL="#toil.test.server.serverTest.ToilWESServerWorkflowTest",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Tests of the WES server running workflows."]; "AbstractToilWESServerTest" -> "ToilWESServerWorkflowTest" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

Test the server with Celery and state stored in S3.

setUp()

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

Return type:

None