Merge branch 'release_20.01' into release_20.05 (3498fcf1) · Commits · NDIP / Galaxy

lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

+1 −1

Original line number	Diff line number	Diff line
		@@ -44,7 +44,7 @@ cmd2==0.8.9
		coloredlogs==14.0
		configparser==4.0.2 ; python_version < '3.2'
		contextlib2==0.6.0.post1 ; python_version < '3.5'
		cryptography==2.9.2
		cryptography==3.2.1
		cwltool==1.0.20191225192155
		debtcollector==1.22.0
		decorator==4.4.2

+1 −0

Original line number	Diff line number	Diff line
		@@ -28,6 +28,7 @@ _galaxy_setup_environment() {
		$integrity_injection
		$slots_statement
		export GALAXY_SLOTS
		export PYTHONWARNINGS="ignore"
		GALAXY_VIRTUAL_ENV="$galaxy_virtual_env"
		_GALAXY_VIRTUAL_ENV="$galaxy_virtual_env"
		PRESERVE_GALAXY_ENVIRONMENT="$preserve_python_environment"

+8 −0

Original line number	Diff line number	Diff line
		@@ -2619,6 +2619,14 @@ simple_mapping(
		simple_mapping(
		model.WorkflowInvocationOutputValue,
		workflow_invocation=relation(model.WorkflowInvocation, backref="output_values"),
		workflow_invocation_step=relation(model.WorkflowInvocationStep,
		foreign_keys=[model.WorkflowInvocationStep.table.c.workflow_invocation_id, model.WorkflowInvocationStep.table.c.workflow_step_id],
		primaryjoin=and_(
		model.WorkflowInvocationStep.table.c.workflow_invocation_id == model.WorkflowInvocationOutputValue.table.c.workflow_invocation_id,
		model.WorkflowInvocationStep.table.c.workflow_step_id == model.WorkflowInvocationOutputValue.table.c.workflow_step_id,
		),
		backref='output_value'
		),
		workflow_step=relation(model.WorkflowStep),
		workflow_output=relation(model.WorkflowOutput),
		)

+6 −10

Original line number	Diff line number	Diff line
		@@ -352,12 +352,6 @@ class WorkflowProgress(object):
		try:
		replacement = step_outputs[output_name]
		except KeyError:
		replacement = self.inputs_by_step_id.get(output_step_id)
		if connection.output_step.type == 'parameter_input' and output_step_id is not None:
		# FIXME: parameter_input step outputs should be properly recorded as step outputs, but for now we can
		# short-circuit and just pick the input value
		pass
		else:
		# Must resolve.
		template = "Workflow evaluation problem - failed to find output_name %s in step_outputs %s"
		message = template % (output_name, step_outputs)
		@@ -428,6 +422,8 @@ class WorkflowProgress(object):

		def set_step_outputs(self, invocation_step, outputs, already_persisted=False):
		step = invocation_step.workflow_step
		if invocation_step.output_value:
		outputs[invocation_step.output_value.workflow_output.output_name] = invocation_step.output_value.value
		self.outputs[step.id] = outputs
		if not already_persisted:
		for output_name, output_object in outputs.items():

+18 −0

Original line number	Diff line number	Diff line
		@@ -2289,6 +2289,24 @@ data_input:
		type: File
		""", history_id=history_id, wait=True, assert_ok=True)

		def test_run_with_int_parameter_nested(self):
		with self.dataset_populator.test_history() as history_id:
		workflow = self.workflow_populator.load_workflow_from_resource("test_subworkflow_with_integer_input")
		workflow_id = self.workflow_populator.create_workflow(workflow)
		hda = self.dataset_populator.new_dataset(history_id, content="1 2 3")
		workflow_request = {
		'history_id': history_id,
		'workflow_id': workflow_id,
		'inputs_by': 'name',
		'inputs': json.dumps({
		'input_dataset': {'src': 'hda', 'id': hda['id']},
		'int_parameter': 1,
		})
		}
		invocation_response = self.workflow_populator.invoke_workflow_raw(workflow_id, workflow_request)
		assert invocation_response.status_code == 200, invocation_response.text
		self.workflow_populator.wait_for_invocation(workflow_id, invocation_response.json()['id'])

		def test_run_with_validated_parameter_connection_default_values(self):
		with self.dataset_populator.test_history() as history_id:
		self._run_jobs(WORKFLOW_PARAMETER_INPUT_INTEGER_DEFAULT, test_data="""