mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
2cd95c48f6
- Add flake8-import-order to flake8 Pipfile and remove py27-lint-imports and py27-lint-imports-include-list tox envs - Fix most E201 and E202 errors reported by flake8-import-order v0.15, but pin flake8-import-order to v0.14.3 until https://github.com/PyCQA/flake8-import-order/issues/123 is fixed This let us drop 2 jobs on Travis per each job.
147 lines
4.4 KiB
Python
147 lines
4.4 KiB
Python
from galaxy import model
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from galaxy.workflow.run_request import (
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_normalize_inputs,
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_normalize_step_parameters
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)
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from .workflow_support import MockTrans
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STEP_ID_OFFSET = 4 # Offset a little so ids and order index are different.
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def test_normalize_parameters_empty():
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normalized_params = __normalize_parameters_against_fixture({})
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assert normalized_params == {}
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def test_normalize_parameters_by_tool():
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normalized_params = __normalize_parameters_against_fixture({
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'cat1': {'foo': 'bar'}
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})
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# Tool specified parameters are expanded out.
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assert normalized_params[STEP_ID_OFFSET + 3] == {'foo': 'bar'}
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assert normalized_params[STEP_ID_OFFSET + 4] == {'foo': 'bar'}
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assert len(normalized_params.keys()) == 2
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def test_step_parameters():
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normalized_params = __normalize_parameters_against_fixture({
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str(STEP_ID_OFFSET + 1): {'foo': 'bar'}
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})
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assert normalized_params[STEP_ID_OFFSET + 1] == {'foo': 'bar'}
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assert len(normalized_params.keys()) == 1
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def test_step_parameters_legacy():
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normalized_params = __normalize_parameters_against_fixture({
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str(STEP_ID_OFFSET + 1): {'param': 'foo', 'value': 'bar'}
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})
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assert normalized_params[STEP_ID_OFFSET + 1] == {'foo': 'bar'}, normalized_params
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assert len(normalized_params.keys()) == 1
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def test_inputs_by_step_id():
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input1 = __new_input()
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input2 = __new_input()
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normalized_inputs = __normalize_inputs_against_fixture({
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str(STEP_ID_OFFSET + 1): input1,
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str(STEP_ID_OFFSET + 2): input2
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}, inputs_by="step_id")
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assert normalized_inputs[STEP_ID_OFFSET + 1]['content'] == input1['content']
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assert normalized_inputs[STEP_ID_OFFSET + 2]['content'] == input2['content']
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def test_inputs_by_step_index():
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input1 = __new_input()
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input2 = __new_input()
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normalized_inputs = __normalize_inputs_against_fixture({
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str(0): input1,
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str(1): input2
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}, inputs_by="step_index")
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assert normalized_inputs[STEP_ID_OFFSET + 1]['content'] == input1['content']
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assert normalized_inputs[STEP_ID_OFFSET + 2]['content'] == input2['content']
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def test_inputs_by_name():
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input1 = __new_input()
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input2 = __new_input()
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normalized_inputs = __normalize_inputs_against_fixture({
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"input1": input1,
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"input2": input2
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}, inputs_by="name")
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assert normalized_inputs[STEP_ID_OFFSET + 1]['content'] == input1['content']
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assert normalized_inputs[STEP_ID_OFFSET + 2]['content'] == input2['content']
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def __normalize_parameters_against_fixture(params):
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trans = MockTrans()
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# Create a throw away workflow so step ids and order_index
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# are different for actual fixture.
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__workflow_fixure(trans)
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workflow = __workflow_fixure(trans)
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normalized_params = _normalize_step_parameters(workflow.steps, params, legacy=True)
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return normalized_params
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def __normalize_inputs_against_fixture(inputs, inputs_by):
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trans = MockTrans()
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# Create a throw away workflow so step ids and order_index
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# are different for actual fixture.
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__workflow_fixure(trans)
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workflow = __workflow_fixure(trans)
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normalized_inputs = _normalize_inputs(workflow.steps, inputs, inputs_by)
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return normalized_inputs
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def __new_input():
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return dict(content=model.HistoryDatasetAssociation())
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def __workflow_fixure(trans):
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user = model.User(
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email="testworkflow_params@bx.psu.edu",
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password="pass"
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)
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stored_workflow = model.StoredWorkflow()
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stored_workflow.user = user
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workflow = model.Workflow()
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workflow.stored_workflow = stored_workflow
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def add_step(**kwds):
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workflow_step = model.WorkflowStep()
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for key, value in kwds.items():
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setattr(workflow_step, key, value)
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workflow.steps.append(workflow_step)
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trans.app.model.context.add(
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workflow,
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)
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add_step(
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type="data_input",
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order_index=0,
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tool_inputs={"name": "input1"}
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)
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add_step(
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type="data_input",
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order_index=1,
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tool_inputs={"name": "input2"}
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)
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add_step(
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type="tool",
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tool_id="cat1",
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order_index=2,
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)
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add_step(
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type="tool",
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tool_id="cat1",
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order_index=4,
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)
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trans.app.model.context.flush()
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# Expunge and reload to ensure step state is as expected from database.
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workflow_id = workflow.id
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trans.app.model.context.expunge_all()
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return trans.app.model.context.query(model.Workflow).get(workflow_id)
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