mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 12:13:33 +08:00
Nicola Soranzo
c35d8f2a06
Also: - Rename `FooBarTestCase` test classes as `TestFooBar`. These were collected by pytest only because they were `unittest.TestCase` derived, but normally pytest collects only test classes whose name starts with `Test`, see https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes
190 lines
6.9 KiB
Python
190 lines
6.9 KiB
Python
from galaxy import model
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from galaxy.app_unittest_utils.tools_support import UsesApp
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from galaxy.tools.parameters import (
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basic,
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dataset_matcher,
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)
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from galaxy.util import (
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bunch,
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XML,
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)
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from galaxy.util.unittest import TestCase
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from .test_data_parameters import MockHistoryDatasetAssociation
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class MockTool:
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def __init__(self, app):
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self.app = app
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self.tool_type = "default"
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self.valid_input_states = model.Dataset.valid_input_states
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class TestDatasetMatcher(TestCase, UsesApp):
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def test_hda_mismatches(self):
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# Datasets not visible are not "valid" for param.
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self.mock_hda.visible = False
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assert not self.test_context.hda_match(self.mock_hda)
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# Datasets that don't match datatype are not valid.
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self.mock_hda.visible = True
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self.mock_hda.extension = "data"
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self.mock_hda.conversion_destination = (False, None, None)
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assert not self.test_context.hda_match(self.mock_hda)
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def test_valid_hda_direct_match(self):
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# Datasets that visible and matching are valid
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self.mock_hda.visible = True
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self.mock_hda.extension = "txt"
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hda_match = self.test_context.hda_match(self.mock_hda, check_implicit_conversions=False)
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assert hda_match
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# Match is not a conversion and so matching hda is the same hda
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# supplied.
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assert not hda_match.implicit_conversion
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assert hda_match.hda == self.mock_hda
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def test_valid_hda_implicit_convered(self):
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# Find conversion returns an HDA to an already implicitly converted
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# dataset.
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self.mock_hda.extension = "data"
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converted_hda = model.HistoryDatasetAssociation()
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self.mock_hda.conversion_destination = (False, "tabular", converted_hda)
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hda_match = self.test_context.hda_match(self.mock_hda)
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assert hda_match
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assert hda_match.implicit_conversion
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assert hda_match.hda == converted_hda
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assert hda_match.target_ext == "tabular"
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def test_hda_match_implicit_can_convert(self):
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# Find conversion returns a target extension to convert to, but not
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# a previously implicitly converted dataset.
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self.mock_hda.extension = "data"
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self.mock_hda.conversion_destination = (False, "tabular", None)
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hda_match = self.test_context.hda_match(self.mock_hda)
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assert hda_match
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assert hda_match.implicit_conversion
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assert hda_match.hda == self.mock_hda
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assert hda_match.target_ext == "tabular"
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def test_hda_match_properly_skips_conversion(self):
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self.mock_hda.extension = "data"
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self.mock_hda.conversion_destination = (False, "tabular", bunch.Bunch())
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hda_match = self.test_context.hda_match(self.mock_hda, check_implicit_conversions=False)
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assert not hda_match
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def test_data_destination_tools_require_public(self):
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self.tool.tool_type = "data_destination"
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# Public datasets okay and valid
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self.app.security_agent.dataset_is_public = lambda dataset: True
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hda_match = self.test_context.hda_match(self.mock_hda)
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assert hda_match
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# Non-public datasets not valid
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self.app.security_agent.dataset_is_public = lambda dataset: False
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hda_match = self.test_context.hda_match(self.mock_hda)
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assert not hda_match
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def test_filtered_hda_matched_key(self):
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self.filtered_param = True
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data1_val = model.HistoryDatasetAssociation()
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data1_val.dbkey = "hg18"
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self.other_values = {"data1": data1_val}
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assert self.test_context.filter_values == {"hg18"}
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# mock_hda is hg19, other is hg18 so should not be "valid hda"
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hda_match = self.test_context.hda_match(self.mock_hda)
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assert not hda_match
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def test_filtered_hda_unmatched_key(self):
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self.filtered_param = True
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data1_val = model.HistoryDatasetAssociation()
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data1_val.dbkey = "hg19"
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self.other_values = {"data1": data1_val}
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# Other param value and this dataset both hg19, should be valid
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hda_match = self.test_context.hda_match(self.mock_hda)
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assert hda_match
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def test_metadata_filtered_hda_options_filter_attribute_matched_keys(self):
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self.metadata_filtered_param = True
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data1_val = model.HistoryDatasetAssociation()
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self.other_values = {"data1": data1_val}
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hda1 = MockHistoryDatasetAssociation()
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hda1.metadata = MockMetadata()
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hda1.metadata.foo = "bar"
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hda2 = MockHistoryDatasetAssociation()
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hda2.metadata = MockMetadata()
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hda2.metadata.foo = "baz"
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assert self.test_context.filter_values == {"baz", "bar"}
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hda_match = self.test_context.hda_match(hda1)
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assert hda_match
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hda_match = self.test_context.hda_match(hda2)
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assert hda_match
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def test_metadata_filtered_hda_options_filter_attribute_unmatched_key(self):
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self.metadata_filtered_param = True
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data1_val = model.HistoryDatasetAssociation()
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self.other_values = {"data1": data1_val}
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hda = MockHistoryDatasetAssociation()
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hda.metadata = MockMetadata()
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hda.metadata.foo = "no-match"
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assert self.test_context.filter_values == {"baz", "bar"}
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hda_match = self.test_context.hda_match(hda)
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assert not hda_match
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def setUp(self):
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self.setup_app()
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self.mock_hda = MockHistoryDatasetAssociation()
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self.tool = MockTool(self.app)
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self.current_user_roles = []
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self.other_values = {}
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# Reset lazily generated stuff
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self.filtered_param = False
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self.metadata_filtered_param = False
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self._test_context = None
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self.param = None
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@property
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def test_context(self):
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if self._test_context is None:
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option_xml = ""
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if self.filtered_param:
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option_xml = """<options><filter type="data_meta" ref="data1" key="dbkey" /></options>"""
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if self.metadata_filtered_param:
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option_xml = """
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<options options_filter_attribute="metadata.foo">
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<filter type="add_value" value="bar" />
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<filter type="add_value" value="baz" />
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</options>"""
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param_xml = XML(f"""<param name="data2" type="data" format="txt">{option_xml}</param>""")
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self.param = basic.DataToolParameter(
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self.tool,
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param_xml,
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)
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trans = bunch.Bunch(
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app=self.app,
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get_current_user_roles=lambda: self.current_user_roles,
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workflow_building_mode=True,
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)
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self._test_context = dataset_matcher.get_dataset_matcher_factory(trans).dataset_matcher(
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param=self.param, other_values=self.other_values
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)
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return self._test_context
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class MockMetadata:
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def __init__(self):
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self.foo = None
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