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mvdbeek
626baad567
Moving this to tools.parameters.workflow_utils avoids a circular dependency when importing is_runtime_value in tools.parameters.dynamic_options.
109 lines
4.8 KiB
Python
109 lines
4.8 KiB
Python
from unittest.mock import Mock
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import pytest
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from galaxy import model
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from galaxy.model.base import transaction
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from galaxy.tools.parameters.workflow_utils import RuntimeValue
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from .util import BaseParameterTestCase
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class TestSelectToolParameter(BaseParameterTestCase):
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def test_validated_values(self):
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self.options_xml = """<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>"""
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with pytest.raises(ValueError) as exc_info:
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self.param.from_json("42", self.trans, {"input_bam": model.HistoryDatasetAssociation()})
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assert str(exc_info.value) == "parameter 'my_name': requires a value, but no legal values defined"
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def test_validated_values_missing_dependency(self):
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self.options_xml = """<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>"""
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with pytest.raises(ValueError) as exc_info:
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self.param.from_json("42", self.trans)
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assert str(exc_info.value) == "parameter 'my_name': requires a value, but no legal values defined"
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def test_unvalidated_values(self):
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self.options_xml = """<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>"""
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self.trans.workflow_building_mode = True
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assert self.param.from_json("42", self.trans) == "42"
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def test_validated_datasets(self):
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self.options_xml = """<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>"""
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with pytest.raises(ValueError) as exc_info:
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self.param.from_json(model.HistoryDatasetAssociation(), self.trans, {"input_bam": None})
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assert str(exc_info.value) == "parameter 'my_name': requires a value, but no legal values defined"
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def test_unvalidated_datasets(self):
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self.options_xml = """<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>"""
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self.trans.workflow_building_mode = True
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assert isinstance(
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self.param.from_json(model.HistoryDatasetAssociation(), self.trans, {"input_bam": RuntimeValue()}),
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model.HistoryDatasetAssociation,
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)
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def test_filter_param_value(self):
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self.options_xml = """<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="0" /></options>"""
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assert ("testname1", "testpath1", False) in self.param.get_options(self.trans, {"input_bam": "testname1"})
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assert ("testname2", "testpath2", False) in self.param.get_options(self.trans, {"input_bam": "testname2"})
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assert len(self.param.get_options(self.trans, {"input_bam": "testname3"})) == 0
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def test_filter_param_value2(self):
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# Same test as above, but filtering on a different column.
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self.options_xml = """<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="1" /></options>"""
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assert ("testname1", "testpath1", False) in self.param.get_options(self.trans, {"input_bam": "testpath1"})
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assert ("testname2", "testpath2", False) in self.param.get_options(self.trans, {"input_bam": "testpath2"})
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assert len(self.param.get_options(self.trans, {"input_bam": "testpath3"})) == 0
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# TODO: Good deal of overlap here with TestDataToolParameter, refactor.
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def setUp(self):
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super().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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session = self.app.model.context
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with transaction(session):
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session.commit()
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self.app.tool_data_tables["test_table"] = MockToolDataTable()
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self.trans = Mock(
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app=self.app,
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get_history=lambda: self.test_history,
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get_current_user_roles=lambda: [],
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workflow_building_mode=False,
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webapp=Mock(name="galaxy"),
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user=None,
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)
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self.type = "select"
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self.set_data_ref = False
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self.multiple = False
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self.optional = False
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self.options_xml = ""
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self._param = None
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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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options_text = self.options_xml
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data_ref_text = ""
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if self.set_data_ref:
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data_ref_text = 'data_ref="input_bam"'
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param_str = f"""<param name="my_name" type="{self.type}" {data_ref_text} {multi_text} {optional_text}>{options_text}</param>"""
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self._param = self._parameter_for(xml=param_str)
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return self._param
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class MockToolDataTable:
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def __init__(self):
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self.columns = dict(
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name=0,
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value=1,
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)
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self.missing_index_file = None
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def get_fields(self):
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return [["testname1", "testpath1"], ["testname2", "testpath2"]]
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