mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
740c4c9344
Only fetch visible datasets into big, cached list of history datasets under consideration. Hidden datasets don't seem to be used by the fetcher or initial value stuff so it seems fine to exclude them. The advantage should be clear for histories with a large number of datasets hidden below a signficantly smaller number collections.
212 lines
8.3 KiB
Python
212 lines
8.3 KiB
Python
from galaxy import model
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from .test_parameter_parsing import BaseParameterTestCase
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from ..unittest_utils import galaxy_mock
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class DataToolParameterTestCase(BaseParameterTestCase):
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def test_to_python_none_values(self):
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assert self.param.to_python(None, self.app) is None
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assert self.param.to_python('None', self.app) is None
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assert self.param.to_python('', self.app) is None
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def test_to_python_hda(self):
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hda = self._new_hda()
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as_python = self.param.to_python(hda.id, self.app)
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assert hda == as_python
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def test_to_python_multi_hdas(self):
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hda1 = self._new_hda()
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hda2 = self._new_hda()
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as_python = self.param.to_python("%s,%s" % (hda1.id, hda2.id), self.app)
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assert as_python == [hda1, hda2]
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def test_to_python_multi_none(self):
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self.multiple = True
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hda = self._new_hda()
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# Selection is Optional. may be selected with other stuff,
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# not sure the UI should really allow this but easy enough
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# to just filter it out.
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self.assertEquals([hda], self.param.to_python('%s,None' % hda.id, self.app))
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def test_field_filter_on_types(self):
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hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
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hda2 = MockHistoryDatasetAssociation(name="hda2", id=2)
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self.stub_active_datasets(hda1, hda2)
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field = self._simple_field()
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assert len(field['options']['hda']) == 2
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assert field['options']['hda'][0]['name'] == "hda2"
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assert field['options']['hda'][1]['name'] == "hda1"
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hda2.extension = 'data'
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field = self._simple_field()
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assert len(field['options']['hda']) == 1, field
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assert field['options']['hda'][0]['name'] == "hda1"
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def test_field_display_hidden_hdas_only_if_selected(self):
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hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
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hda2 = MockHistoryDatasetAssociation(name="hda2", id=2)
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hda1.visible = False
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hda2.visible = False
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self.stub_active_datasets(hda1, hda2)
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field = self._simple_field(other_values={"data2" : hda2})
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assert len(field['options']['hda']) == 1 # hda1 not an option, not visible or selected
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assert field['options']['hda'][0]['name'] == "(hidden) hda2"
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def test_field_display_deleted_hdas_only_if_selected(self):
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hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
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hda2 = MockHistoryDatasetAssociation(name="hda2", id=2)
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hda1.visible = False
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hda2.deleted = True
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self.stub_active_datasets(hda1, hda2)
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field = self._simple_field(other_values={"data2" : hda2})
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assert len(field['options']['hda']) == 1 # hda1 not an option, not visible or selected
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assert field['options']['hda'][0]['name'] == "(deleted) hda2"
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def test_field_implicit_conversion_new(self):
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hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
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hda1.extension = 'data'
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hda1.conversion_destination = ("tabular", None)
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self.stub_active_datasets(hda1)
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field = self._simple_field()
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assert len(field['options']['hda']) == 1
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assert field['options']['hda'][0]['name'] == "hda1 (as tabular)"
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assert field['options']['hda'][0]['hid'] == 1
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def test_field_implicit_conversion_existing(self):
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hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
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hda1.extension = 'data'
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hda1.conversion_destination = ("tabular", MockHistoryDatasetAssociation(name="hda1converted", id=2))
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self.stub_active_datasets(hda1)
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field = self._simple_field()
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assert len(field['options']['hda']) == 1
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assert field['options']['hda'][0]['name'] == "hda1 (as tabular)"
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# This is difference with previous test, value is existing
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# hda id not new one.
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assert field['options']['hda'][0]['hid'] == 2
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def test_field_multiple(self):
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self.multiple = True
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field = self._simple_field()
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assert field['multiple']
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def test_field_empty_selection(self):
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field = self._simple_field()
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assert len(field['options']['hda']) == 0
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assert len(field['options']['hdca']) == 0
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def test_field_empty_selection_optional(self):
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self.optional = True
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field = self._simple_field()
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assert field['optional']
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def test_get_initial_value(self):
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hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
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hda2 = MockHistoryDatasetAssociation(name="hda2", id=2)
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self.stub_active_datasets(hda1, hda2)
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assert hda2 == self.param.get_initial_value(self.trans, {})
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def test_get_initial_value_is_none_if_no_match(self):
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hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
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hda1.visible = False
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hda2 = MockHistoryDatasetAssociation(name="hda2", id=2)
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hda2.visible = False
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self.stub_active_datasets(hda1, hda2)
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assert self.param.get_initial_value(self.trans, {}) is None
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def test_get_initial_none_when_optional(self):
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self.optional = True
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hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
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hda2 = MockHistoryDatasetAssociation(name="hda2", id=2)
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self.stub_active_datasets(hda1, hda2)
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assert self.param.get_initial_value(self.trans, {}) is None
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def test_get_initial_with_previously_converted_data(self):
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hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
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hda1.extension = 'data'
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converted = MockHistoryDatasetAssociation(name="hda1converted", id=2)
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hda1.conversion_destination = ("tabular", converted)
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self.stub_active_datasets(hda1)
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assert converted == self.param.get_initial_value(self.trans, {})
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def test_get_initial_with_to_be_converted_data(self):
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hda1 = MockHistoryDatasetAssociation(name="hda1", id=1)
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hda1.extension = 'data'
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hda1.conversion_destination = ("tabular", None)
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self.stub_active_datasets(hda1)
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assert hda1 == self.param.get_initial_value(self.trans, {}), hda1
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def _new_hda(self):
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hda = model.HistoryDatasetAssociation()
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hda.visible = True
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hda.dataset = model.Dataset()
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self.app.model.context.add(hda)
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self.app.model.context.flush()
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return hda
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def setUp(self):
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super(DataToolParameterTestCase, self).setUp()
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self.test_history = model.History()
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self.app.model.context.add(self.test_history)
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self.app.model.context.flush()
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self.trans = galaxy_mock.MockTrans(history=self.test_history)
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self.multiple = False
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self.optional = False
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self._param = None
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def stub_active_datasets(self, *hdas):
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self.test_history._active_datasets_and_roles = [h for h in hdas if not h.deleted]
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self.test_history._active_visible_datasets_and_roles = [h for h in hdas if not h.deleted and h.visible]
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def _simple_field(self, **kwds):
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return self.param.to_dict(trans=self.trans, **kwds)
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@property
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def param(self):
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if not self._param:
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multi_text = ""
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if self.multiple:
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multi_text = 'multiple="True"'
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optional_text = ""
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if self.optional:
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optional_text = 'optional="True"'
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template_xml = '''<param name="data2" type="data" format="txt" %s %s></param>'''
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param_str = template_xml % (multi_text, optional_text)
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self._param = self._parameter_for(tool=self.mock_tool, xml=param_str)
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return self._param
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class MockHistoryDatasetAssociation(object):
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""" Fake HistoryDatasetAssociation stubbed out for testing matching and
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stuff like that.
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"""
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def __init__(self, test_dataset=None, name="Test Dataset", id=1):
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if not test_dataset:
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test_dataset = model.Dataset()
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test_dataset.state = model.Dataset.states.OK
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self.states = model.HistoryDatasetAssociation.states
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self.deleted = False
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self.dataset = test_dataset
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self.visible = True
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self.conversion_destination = (None, None)
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self.extension = "txt"
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self.dbkey = "hg19"
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self.implicitly_converted_parent_datasets = False
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self.name = name
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self.hid = id
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self.id = id
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self.children = []
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self.tags = []
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@property
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def state(self):
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return self.dataset.state
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def get_dbkey(self):
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return self.dbkey
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def find_conversion_destination(self, formats):
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return self.conversion_destination
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