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https://github.com/galaxyproject/galaxy.git
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mvdbeek
3056fbbf12
This obviously doesn't work (yet) with filters that work on the input dataset, but this already removes a lot of outputs that arent' going to be produced based on static options. Since exceptions default to priduing the dataset this isn't much harm.
299 lines
8.9 KiB
Python
299 lines
8.9 KiB
Python
import json
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import mock
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from galaxy import model
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from galaxy.util import bunch
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from galaxy.workflow import modules
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from .workflow_support import MockTrans, yaml_to_model
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def test_input_has_no_errors():
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trans = MockTrans()
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input_step_module = modules.module_factory.from_dict(trans, {"type": "data_input"})
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assert not input_step_module.get_errors()
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def test_valid_new_tool_has_no_errors():
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trans = MockTrans()
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mock_tool = __mock_tool()
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trans.app.toolbox.tools["cat1"] = mock_tool
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tool_module = modules.module_factory.from_dict(trans, {"type": "tool", "tool_id": "cat1"})
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assert not tool_module.get_errors()
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def test_data_input_default_state():
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trans = MockTrans()
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module = modules.module_factory.from_dict(trans, {"type": "data_input", "label": "Input Dataset"})
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__assert_has_runtime_input(module, label="Input Dataset")
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def test_data_input_modified_state():
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module = __from_state({"type": "data_input", "label": "Cool Input"})
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__assert_has_runtime_input(module, label="Cool Input")
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def test_data_input_step_modified_state():
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module = __from_step(type="data_input", label="Cool Input")
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__assert_has_runtime_input(module, label="Cool Input")
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def test_data_input_compute_runtime_state_default():
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module = __from_step(type="data_input")
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state, errors = module.compute_runtime_state(module.trans, module.test_step)
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assert not errors
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assert "input" in state.inputs
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assert state.inputs["input"] is None
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def test_data_input_compute_runtime_state_args():
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module = __from_step(type="data_input")
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tool_state = module.get_state()
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hda = model.HistoryDatasetAssociation()
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with mock.patch("galaxy.workflow.modules.check_param") as check_method:
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check_method.return_value = (hda, None)
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state, errors = module.compute_runtime_state(module.trans, module.test_step, {"input": 4, "tool_state": tool_state})
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assert not errors
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assert "input" in state.inputs
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assert state.inputs["input"] is hda
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def test_data_input_connections():
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module = __from_step(type="data_input")
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assert len(module.get_data_inputs()) == 0
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outputs = module.get_data_outputs()
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assert len(outputs) == 1
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output = outputs[0]
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assert output["name"] == "output"
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assert output["extensions"] == ["input"]
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def test_data_collection_input_default_state():
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trans = MockTrans()
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module = modules.module_factory.from_dict(trans, {"type": "data_collection_input", "label": "Input Dataset Collection"})
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__assert_has_runtime_input(module, label="Input Dataset Collection", collection_type="list")
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def test_data_input_collection_modified_state():
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module = __from_state({
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"type": "data_collection_input",
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"label": "Cool Input Collection",
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"tool_state": json.dumps({"collection_type": "list:paired"}),
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})
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__assert_has_runtime_input(module, label="Cool Input Collection", collection_type="list:paired")
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def test_data_input_collection_step_modified_state():
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module = __from_step(
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type="data_collection_input",
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label="Cool Input Collection",
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tool_inputs={
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"collection_type": "list:paired",
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},
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)
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__assert_has_runtime_input(module, label="Cool Input Collection", collection_type="list:paired")
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def test_data_collection_input_connections():
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module = __from_step(
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type="data_collection_input",
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tool_inputs={
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"collection_type": "list:paired"
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}
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)
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assert len(module.get_data_inputs()) == 0
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outputs = module.get_data_outputs()
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assert len(outputs) == 1
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output = outputs[0]
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assert output["name"] == "output"
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assert output["extensions"] == ["input_collection"]
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assert output["collection_type"] == "list:paired"
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def test_data_collection_input_config_form():
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module = __from_step(
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type="data_collection_input",
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tool_inputs={
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"collection_type": "list:paired",
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}
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)
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result = module.get_config_form()
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assert result["inputs"][0]["value"], "list:paired"
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def test_cannot_create_tool_modules_for_missing_tools():
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trans = MockTrans()
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module = modules.module_factory.from_dict(trans, {"type": "tool", "tool_id": "cat1"})
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assert not module.tool
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def test_updated_tool_version():
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trans = MockTrans()
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mock_tool = __mock_tool(id="cat1", version="0.9")
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trans.app.toolbox.tools["cat1"] = mock_tool
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module = __from_step(
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trans=trans,
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type="tool",
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tool_id="cat1",
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tool_version="0.7",
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config=None,
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)
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# Make sure there is a warnin with tool id, old version,
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# and new version.
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for val in "cat1", "0.7", "0.9":
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assert val in module.version_changes[0]
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def test_tool_version_same():
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trans = MockTrans()
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mock_tool = __mock_tool(id="cat1", version="1.0")
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trans.app.toolbox.tools["cat1"] = mock_tool
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module = __from_step(
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trans=trans,
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type="tool",
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tool_id="cat1",
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tool_version="1.0",
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config=None,
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)
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assert not module.version_changes
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TEST_WORKFLOW_YAML = """
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steps:
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- type: "data_input"
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label: "input1"
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- type: "data_collection_input"
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label: "input2"
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- type: "tool"
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tool_id: "cat1"
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inputs:
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input1:
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connections:
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- "@output_step": 0
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output_name: "output"
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- type: "tool"
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tool_id: "cat1"
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inputs:
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input1:
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connections:
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- "@output_step": 0
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output_name: "output"
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workflow_outputs:
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- output_name: "out_file1"
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label: "out1"
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- type: "tool"
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tool_id: "cat1"
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inputs:
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input1:
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connections:
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- "@output_step": 2
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output_name: "out_file1"
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workflow_outputs:
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- output_name: "out_file1"
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"""
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def test_subworkflow_new_inputs():
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subworkflow_module = __new_subworkflow_module()
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inputs = subworkflow_module.get_data_inputs()
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assert len(inputs) == 2, len(inputs)
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input1, input2 = inputs
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assert input1["input_type"] == "dataset"
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assert input1["name"] == "input1"
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assert input2["input_type"] == "dataset_collection"
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assert input2["name"] == "input2", input2["name"]
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def test_subworkflow_new_outputs():
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subworkflow_module = __new_subworkflow_module()
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outputs = subworkflow_module.get_data_outputs()
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assert len(outputs) == 2, len(outputs)
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output1, output2 = outputs
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assert output1["name"] == "out1"
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assert output1["label"] == "out1"
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assert output1["extensions"] == ["input"]
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assert output2["name"] == "4:out_file1", output2["name"]
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assert output2["label"] == "4:out_file1", output2["label"]
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def __new_subworkflow_module():
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trans = MockTrans()
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mock_tool = __mock_tool(id="cat1", version="1.0")
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trans.app.toolbox.tools["cat1"] = mock_tool
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workflow = yaml_to_model(TEST_WORKFLOW_YAML)
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stored_workflow = trans.save_workflow(workflow)
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workflow_id = trans.app.security.encode_id(stored_workflow.id)
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subworkflow_module = modules.module_factory.from_dict(trans, {"type": "subworkflow", "content_id": workflow_id})
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return subworkflow_module
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def __assert_has_runtime_input(module, label=None, collection_type=None):
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inputs = module.get_runtime_inputs()
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assert len(inputs) == 1
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assert "input" in inputs
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input_param = inputs["input"]
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if label is not None:
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assert input_param.get_label() == label, input_param.get_label()
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if collection_type is not None:
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assert input_param.collection_types == [collection_type]
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return input_param
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def __from_state(state):
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trans = MockTrans()
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module = modules.module_factory.from_dict(trans, state)
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return module
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def __from_step(**kwds):
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if "trans" in kwds:
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trans = kwds["trans"]
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del kwds["trans"]
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else:
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trans = MockTrans()
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step = __step(
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**kwds
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)
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injector = modules.WorkflowModuleInjector(trans)
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injector.inject(step, exact_tools=False)
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module = step.module
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module.test_step = step
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return module
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def __step(**kwds):
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step = model.WorkflowStep()
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for key, value in kwds.items():
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setattr(step, key, value)
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return step
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def __mock_tool(
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id="cat1",
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version="1.0",
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):
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# For now ignoring inputs, params_from_strings, and
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# check_and_update_param_values since only have unit tests for version
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# handling - but need to write tests for all of this longer term.
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tool = bunch.Bunch(
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id=id,
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version=version,
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name=id,
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inputs={},
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outputs={'out_file1': bunch.Bunch(collection=None,
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format='input',
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format_source=None,
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change_format=[],
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filters=[],
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label=None)},
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params_from_strings=mock.Mock(),
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check_and_update_param_values=mock.Mock(),
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to_json=_to_json
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)
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return tool
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def _to_json(*args, **kwargs):
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return "{}"
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