from typing import ( Any, Optional, ) from galaxy import model from galaxy.app_unittest_utils import galaxy_mock from .util import BaseParameterTestCase class TestDataToolParameter(BaseParameterTestCase): def test_to_python_none_values(self): assert self.param.to_python(None, self.app) is None assert self.param.to_python("None", self.app) is None assert self.param.to_python("", self.app) is None def test_to_python_hda(self): hda = self._new_hda() as_python = self.param.to_python(hda.id, self.app) assert hda == as_python def test_to_python_multi_hdas(self): hda1 = self._new_hda() hda2 = self._new_hda() as_python = self.param.to_python(f"{hda1.id},{hda2.id}", self.app) assert as_python == [hda1, hda2] def test_to_python_multi_none(self): self.multiple = True hda = self._new_hda() # Selection is Optional. may be selected with other stuff, # not sure the UI should really allow this but easy enough # to just filter it out. assert [hda] == self.param.to_python(f"{hda.id},None", self.app) def test_field_filter_on_types(self): hda1 = MockHistoryDatasetAssociation(name="hda1", id=1) hda2 = MockHistoryDatasetAssociation(name="hda2", id=2) self.stub_active_datasets(hda1, hda2) field = self._simple_field() assert len(field["options"]["hda"]) == 2 assert field["options"]["hda"][0]["name"] == "hda2" assert field["options"]["hda"][1]["name"] == "hda1" hda2.extension = "data" hda2.conversion_destination = (False, None, None) field = self._simple_field() assert len(field["options"]["hda"]) == 1, field assert field["options"]["hda"][0]["name"] == "hda1" def test_field_display_hidden_hdas_only_if_selected(self): hda1 = MockHistoryDatasetAssociation(name="hda1", id=1) hda2 = MockHistoryDatasetAssociation(name="hda2", id=2) hda1.visible = False hda2.visible = False self.stub_active_datasets(hda1, hda2) field = self._simple_field(other_values={"data2": hda2}) assert len(field["options"]["hda"]) == 1 # hda1 not an option, not visible or selected assert field["options"]["hda"][0]["name"] == "(hidden) hda2" def test_field_display_deleted_hdas_only_if_selected(self): hda1 = MockHistoryDatasetAssociation(name="hda1", id=1) hda2 = MockHistoryDatasetAssociation(name="hda2", id=2) hda1.visible = False hda2.deleted = True self.stub_active_datasets(hda1, hda2) field = self._simple_field(other_values={"data2": hda2}) assert len(field["options"]["hda"]) == 1 # hda1 not an option, not visible or selected assert field["options"]["hda"][0]["name"] == "(deleted) hda2" def test_field_implicit_conversion_new(self): hda1 = MockHistoryDatasetAssociation(name="hda1", id=1) hda1.extension = "data" hda1.conversion_destination = (False, "tabular", None) self.stub_active_datasets(hda1) field = self._simple_field() assert len(field["options"]["hda"]) == 1 assert field["options"]["hda"][0]["name"] == "hda1 (as tabular)" assert field["options"]["hda"][0]["hid"] == 1 def test_field_implicit_conversion_existing(self): hda1 = MockHistoryDatasetAssociation(name="hda1", id=1) hda1.extension = "data" hda1.conversion_destination = (False, "tabular", MockHistoryDatasetAssociation(name="hda1converted", id=2)) self.stub_active_datasets(hda1) field = self._simple_field() assert len(field["options"]["hda"]) == 1 assert field["options"]["hda"][0]["name"] == "hda1 (as tabular)" # This is difference with previous test, value is existing # hda id not new one. assert field["options"]["hda"][0]["hid"] == 2 def test_field_multiple(self): self.multiple = True field = self._simple_field() assert field["multiple"] def test_field_empty_selection(self): field = self._simple_field() assert len(field["options"]["hda"]) == 0 assert len(field["options"]["hdca"]) == 0 def test_field_empty_selection_optional(self): self.optional = True field = self._simple_field() assert field["optional"] def test_get_initial_value(self): hda1 = MockHistoryDatasetAssociation(name="hda1", id=1) hda2 = MockHistoryDatasetAssociation(name="hda2", id=2) self.stub_active_datasets(hda1, hda2) assert hda2 == self.param.get_initial_value(self.trans, {}) def test_get_initial_value_is_none_if_no_match(self): hda1 = MockHistoryDatasetAssociation(name="hda1", id=1) hda1.visible = False hda2 = MockHistoryDatasetAssociation(name="hda2", id=2) hda2.visible = False self.stub_active_datasets(hda1, hda2) assert self.param.get_initial_value(self.trans, {}) is None def test_get_initial_none_when_optional(self): self.optional = True hda1 = MockHistoryDatasetAssociation(name="hda1", id=1) hda2 = MockHistoryDatasetAssociation(name="hda2", id=2) self.stub_active_datasets(hda1, hda2) assert self.param.get_initial_value(self.trans, {}) is None def test_get_initial_with_previously_converted_data(self): hda1 = MockHistoryDatasetAssociation(name="hda1", id=1) hda1.extension = "data" converted = MockHistoryDatasetAssociation(name="hda1converted", id=2) hda1.conversion_destination = (False, "tabular", converted) self.stub_active_datasets(hda1) assert converted == self.param.get_initial_value(self.trans, {}) def test_get_initial_with_to_be_converted_data(self): hda1 = MockHistoryDatasetAssociation(name="hda1", id=1) hda1.extension = "data" hda1.conversion_destination = (False, "tabular", None) self.stub_active_datasets(hda1) assert hda1 == self.param.get_initial_value(self.trans, {}), hda1 def _new_hda(self): hda = model.HistoryDatasetAssociation() hda.visible = True hda.dataset = model.Dataset() session = self.app.model.context session.add(hda) session.commit() return hda def setUp(self): super().setUp() self.test_history = model.History() session = self.app.model.context session.add(self.test_history) session.commit() self.trans = galaxy_mock.MockTrans(history=self.test_history) self.multiple = False self.optional = False self._param = None def stub_active_datasets(self, *hdas): self.test_history._active_datasets_and_roles = [h for h in hdas if not h.deleted] self.test_history._active_visible_datasets_and_roles = [h for h in hdas if not h.deleted and h.visible] def _simple_field(self, **kwds): return self.param.to_dict(trans=self.trans, **kwds) @property def param(self): if not self._param: multi_text = "" if self.multiple: multi_text = 'multiple="True"' optional_text = "" if self.optional: optional_text = 'optional="True"' param_str = f"""""" self._param = self._parameter_for(tool=self.mock_tool, xml=param_str) return self._param class MockHistoryDatasetAssociation: """Fake HistoryDatasetAssociation stubbed out for testing matching and stuff like that. """ def __init__(self, test_dataset=None, name="Test Dataset", id=1): if not test_dataset: test_dataset = model.Dataset() test_dataset.state = model.Dataset.states.OK self.states = model.HistoryDatasetAssociation.states self.deleted = False self.dataset = test_dataset self.visible = True self.conversion_destination: tuple[bool, Optional[str], Optional[Any]] = (True, None, None) self.extension = "txt" self.dbkey = "hg19" self.implicitly_converted_parent_datasets = False self.name = name self.hid = id self.id = id self.tags = [] self.metadata = None @property def state(self): return self.dataset.state def get_dbkey(self): return self.dbkey def find_conversion_destination(self, formats): return self.conversion_destination