def create_valid_pipeline(self):
p = Pipeline(family=PipelineFamily())
self.add_inputs(p, self.create_input(datatypes.STR_PK, dataset_idx=1))
m = Method()
m.method = m
self.add_inputs(m, self.create_input(datatypes.STR_PK, dataset_idx=1))
self.add_outputs(m, self.create_output(datatypes.STR_PK,
dataset_idx=1))
step1 = PipelineStep(pipeline=p, transformation=m, step_num=1)
p.steps.add(step1)
cable = PipelineStepInputCable(pipelinestep=step1,
source_step=0,
source=p.inputs.all()[0],
dest=m.inputs.all()[0])
cable.pipelinestepinputcable = cable
step1.cables_in.add(cable)
outcable = PipelineOutputCable(pipeline=p,
output_idx=1,
source_step=1,
source=m.outputs.all()[0],
output_cdt=m.outputs.all()[0].get_cdt())
p.outcables.add(outcable)
yield p
def test_pipeline_many_valid_inputs_clean(self):
"""A Pipeline with multiple, properly indexed inputs is clean."""
p = Pipeline(family=PipelineFamily())
self.add_inputs(p, TransformationInput(dataset_idx=2),
TransformationInput(dataset_idx=1),
TransformationInput(dataset_idx=3))
p.clean()
def test_pipeline_one_invalid_input_clean(self):
"""A Pipeline with one input not numbered "1" is not clean."""
p = Pipeline(family=PipelineFamily())
self.add_inputs(p, TransformationInput(dataset_idx=4))
error = "Inputs are not consecutively numbered starting from 1"
self.assertRaisesRegexp(ValidationError, error, p.clean)
self.assertRaisesRegexp(ValidationError, error, p.complete_clean)
def test_pipeline_no_inputs_no_steps(self):
"""A Pipeline with no inputs and no steps is clean but not complete."""
p = Pipeline(family=PipelineFamily())
p.clean()
self.assertRaisesRegexp(
ValidationError, re.escape("Pipeline {} has no steps".format(p)),
p.complete_clean)
def test_pipeline_many_invalid_inputs_clean(self):
"""A Pipeline with multiple, badly indexed inputs is not clean."""
p = Pipeline(family=PipelineFamily())
self.add_inputs(p, TransformationInput(dataset_idx=2),
TransformationInput(dataset_idx=3),
TransformationInput(dataset_idx=4))
self.assertRaisesRegexp(
ValidationError,
"Inputs are not consecutively numbered starting from 1", p.clean)
def test_pipeline_one_valid_input_no_steps(self):
"""A Pipeline with one valid input, but no steps, is clean but not complete."""
p = Pipeline(family=PipelineFamily())
self.add_inputs(p, TransformationInput(dataset_idx=1))
p.clean()
self.assertRaisesRegexp(
ValidationError, re.escape("Pipeline {} has no steps".format(p)),
p.complete_clean)
def __init__(self, *args, **kwargs):
super(PipelineSerializer, self).__init__(*args, **kwargs)
# Set the querysets of the related model fields.
curr_user = self.context["request"].user
# LOGGER.debug("PL SERIALIZER INIT %s" % self.context.get("only_is_published", False))
revision_parent_field = self.fields["revision_parent"]
revision_parent_field.queryset = Pipeline.filter_by_user(curr_user)
family_field = self.fields["family"]
family_field.queryset = PipelineFamily.filter_by_user(curr_user)
def test_pipeline_many_valid_steps_clean(self):
"""Test step index check, well-indexed multi-step case."""
p = Pipeline(family=PipelineFamily())
self.add_inputs(p, TransformationInput(dataset_idx=1))
m = Method()
self.add_inputs(m, TransformationInput(dataset_idx=1))
p.steps.add(PipelineStep(pipeline=p, transformation=m, step_num=2))
p.steps.add(PipelineStep(pipeline=p, transformation=m, step_num=1))
p.steps.add(PipelineStep(pipeline=p, transformation=m, step_num=3))
p.clean()
def test_pipeline_many_invalid_steps_clean(self):
"""Test step index check, badly-indexed multi-step case."""
p = Pipeline(family=PipelineFamily())
self.add_inputs(p, TransformationInput(dataset_idx=1))
m = Method()
self.add_inputs(m, TransformationInput(dataset_idx=1))
p.steps.add(PipelineStep(pipeline=p, transformation=m, step_num=1))
p.steps.add(PipelineStep(pipeline=p, transformation=m, step_num=4))
p.steps.add(PipelineStep(pipeline=p, transformation=m, step_num=5))
self.assertRaisesRegexp(
ValidationError,
"Steps are not consecutively numbered starting from 1", p.clean)
def test_build_removal_plan_for_used_image(self):
image = DockerImage(id=99, name='doomed')
method = image.methods.create(transformation_ptr_id=100)
step = method.pipelinesteps.create(id=101)
step.pipeline = Pipeline(transformation_ptr_id=102)
step.pipeline.family = PipelineFamily()
expected_plan = empty_removal_plan()
expected_plan['DockerImages'].add(image)
expected_plan['Methods'].add(method)
expected_plan['Pipelines'].add(step.pipeline)
plan = image.build_removal_plan()
self.assertEqual(expected_plan, plan)
def test_pipeline_oneStep_invalid_cabling_incorrect_cdt_clean(self):
"""Bad cabling: input is of wrong CompoundDatatype."""
p = Pipeline(family=PipelineFamily())
self.add_inputs(p, self.create_input(datatypes.INT_PK, dataset_idx=1))
m = Method()
self.add_inputs(m, self.create_input(datatypes.STR_PK, dataset_idx=1))
step1 = PipelineStep(pipeline=p, transformation=m, step_num=1)
p.steps.add(step1)
cable = PipelineStepInputCable(pipelinestep=step1,
source_step=0,
source=p.inputs.all()[0],
dest=m.inputs.all()[0])
cable.pipelinestepinputcable = cable
step1.cables_in.add(cable)
cable.clean()
self.assertRaisesRegexp(
ValidationError,
'Custom wiring required for cable "{}"'.format(cable),
cable.clean_and_completely_wired)