mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 12:13:33 +08:00
Nicola Soranzo
9d74bba7fb
Upgrade syntax using `pyupgrade --py36-plus` . Manually drop several `six` imports. Also: - Remove broken pr_cache in scripts/bootstrap_history.py - Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
301 lines
10 KiB
Python
301 lines
10 KiB
Python
import os
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import tempfile
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import pytest
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from galaxy.datatypes.metadata import MetadataSpecCollection
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from galaxy.job_execution.datasets import DatasetPath
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from galaxy.tools.parameters.basic import (
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BooleanToolParameter,
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DrillDownSelectToolParameter,
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FloatToolParameter,
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IntegerToolParameter,
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SelectToolParameter,
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TextToolParameter,
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)
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from galaxy.tools.wrappers import (
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DatasetFilenameWrapper,
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InputValueWrapper,
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RawObjectWrapper,
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SelectToolParameterWrapper
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)
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from galaxy.util import XML
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from galaxy.util.bunch import Bunch
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def with_mock_tool(func):
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def call():
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test_directory = tempfile.mkdtemp()
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app = MockApp(test_directory)
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tool = MockTool(app)
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return func(tool)
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call.__name__ = func.__name__
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return call
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def selectwrapper(tool, value, multiple=False, optional=False):
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optional = 'optional="true"' if optional else ''
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multiple = 'multiple="true"' if multiple else ''
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xml = XML('''<param name="blah" type="select" {} {}>
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<option value="x">I am X</option>
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<option value="y" selected="true">I am Y</option>
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<option value="z">I am Z</option>
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</param>'''.format(multiple, optional))
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parameter = SelectToolParameter(tool, xml)
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return SelectToolParameterWrapper(parameter, value)
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@with_mock_tool
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def test_select_wrapper_simple_options(tool):
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wrapper = selectwrapper(tool, "x")
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assert wrapper.name == "blah"
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assert str(wrapper) == "x"
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assert wrapper.value_label == "I am X"
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wrapper = selectwrapper(tool, None, optional=True)
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assert str(wrapper) == "None"
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assert wrapper == ""
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assert wrapper == "None"
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@with_mock_tool
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def test_select_wrapper_multiple_options(tool):
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wrapper = selectwrapper(tool, ["x"], multiple=True)
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assert wrapper.name == "blah"
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assert str(wrapper) == "x"
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assert "x" in wrapper
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wrapper = selectwrapper(tool, ["x", "z"], multiple=True)
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assert str(wrapper) == "x,z"
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assert "x" in wrapper
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wrapper = selectwrapper(tool, [], multiple=True)
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assert str(wrapper) == "None"
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assert wrapper == ""
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assert wrapper == "None"
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assert "x" not in wrapper
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@with_mock_tool
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def test_select_wrapper_with_drilldown(tool):
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parameter = _drilldown_parameter(tool)
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wrapper = SelectToolParameterWrapper(parameter, ["option3"])
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assert str(wrapper) == "option3", str(wrapper)
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@with_mock_tool
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def test_select_wrapper_option_file(tool):
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parameter = _setup_blast_tool(tool)
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wrapper = SelectToolParameterWrapper(parameter, "val2")
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assert str(wrapper) == "val2"
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assert wrapper.fields.name == "name2"
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assert wrapper.fields.path == "path2"
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@with_mock_tool
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def test_select_wrapper_multiple(tool):
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parameter = _setup_blast_tool(tool, multiple=True)
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wrapper = SelectToolParameterWrapper(parameter, ["val1", "val2"])
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assert str(wrapper) == "val1,val2"
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assert wrapper.fields.name == "name1,name2"
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@with_mock_tool
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def test_select_wrapper_with_path_rewritting(tool):
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parameter = _setup_blast_tool(tool, multiple=True)
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compute_environment = MockComputeEnvironment(None)
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wrapper = SelectToolParameterWrapper(parameter, ["val1", "val2"], other_values={}, compute_environment=compute_environment)
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assert wrapper.fields.path == "Rewrite<path1>,Rewrite<path2>"
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def test_raw_object_wrapper():
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obj = Bunch(x=4)
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wrapper = RawObjectWrapper(obj)
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assert wrapper.x == 4
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assert wrapper
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false_wrapper = RawObjectWrapper(False)
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assert not false_wrapper
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def valuewrapper(tool, value, paramtype, optional=False):
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if paramtype == "integer":
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optional = 'optional="true"' if optional else 'value="10"'
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parameter = IntegerToolParameter(tool, XML('<param name="blah" type="integer" %s min="0" />' % optional))
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elif paramtype == "text":
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optional = 'optional="true"' if optional else 'value="foo"'
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parameter = TextToolParameter(tool, XML('<param name="blah" type="text" %s/>' % optional))
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elif paramtype == "float":
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optional = 'optional="true"' if optional else 'value="10.0"'
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parameter = FloatToolParameter(tool, XML('<param name="blah" type="float" %s/>' % optional))
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elif paramtype == "boolean":
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optional = 'optional="true"' if optional else 'value=""'
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parameter = BooleanToolParameter(tool, XML('<param name="blah" type="boolean" truevalue="truevalue" falsevalue="falsevalue" %s/>' % optional))
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return InputValueWrapper(parameter, value)
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@with_mock_tool
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def test_input_value_wrapper_comparison(tool):
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wrapper = valuewrapper(tool, 5, "integer")
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assert str(wrapper) == "5"
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assert int(wrapper) == 5
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assert wrapper != "5"
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assert wrapper == 5
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assert wrapper == 5.0
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assert wrapper > 2
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assert wrapper < 10
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assert wrapper < 5.1
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wrapper = valuewrapper(tool, True, "boolean")
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assert bool(wrapper) is True, wrapper
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assert str(wrapper) == "truevalue"
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assert wrapper == "truevalue"
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wrapper = valuewrapper(tool, False, "boolean")
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assert bool(wrapper) is False, wrapper
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assert str(wrapper) == "falsevalue"
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assert wrapper == "falsevalue"
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@with_mock_tool
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def test_input_value_wrapper_comparison_optional(tool):
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wrapper = valuewrapper(tool, None, 'integer', optional=True)
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assert not wrapper
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with pytest.raises(ValueError):
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int(wrapper)
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assert str(wrapper) == ""
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assert wrapper == "" # for backward-compatibility
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wrapper = valuewrapper(tool, 0, 'integer', optional=True)
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assert wrapper == 0
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assert int(wrapper) == 0
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assert str(wrapper)
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assert wrapper != "" # for backward-compatibility, the correct way to check if an optional integer param is not empty is to use str(wrapper)
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wrapper = valuewrapper(tool, None, 'integer', optional=True)
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assert wrapper != 1
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assert str(wrapper) == ""
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assert wrapper == None # noqa: E711
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wrapper = valuewrapper(tool, None, "boolean")
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assert bool(wrapper) is False, wrapper
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assert str(wrapper) == 'falsevalue'
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@with_mock_tool
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def test_input_value_wrapper_input_value_wrapper_comparison(tool):
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wrapper = valuewrapper(tool, 5, "integer")
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assert str(wrapper) == valuewrapper(tool, "5", "text")
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assert int(wrapper) == valuewrapper(tool, "5", "integer")
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assert wrapper != valuewrapper(tool, "5", "text")
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assert wrapper == valuewrapper(tool, "5", "integer")
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assert wrapper == valuewrapper(tool, "5", "float")
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assert wrapper > valuewrapper(tool, "2", "integer")
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assert wrapper < valuewrapper(tool, "10", "integer")
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assert wrapper < valuewrapper(tool, "5.1", "float")
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def test_dataset_wrapper():
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dataset = MockDataset()
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wrapper = DatasetFilenameWrapper(dataset)
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assert str(wrapper) == MOCK_DATASET_PATH
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assert wrapper.file_name == MOCK_DATASET_PATH
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assert wrapper.ext == MOCK_DATASET_EXT
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def test_dataset_wrapper_false_path():
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dataset = MockDataset()
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new_path = "/new/path/dataset_123.dat"
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wrapper = DatasetFilenameWrapper(dataset, compute_environment=MockComputeEnvironment(false_path=new_path))
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assert str(wrapper) == new_path
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assert wrapper.file_name == new_path
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class MockComputeEnvironment:
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def __init__(self, false_path, false_extra_files_path=None):
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self.false_path = false_path
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self.false_extra_files_path = false_extra_files_path
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def input_path_rewrite(self, dataset):
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return self.false_path
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def input_extra_files_rewrite(self, dataset):
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return self.false_extra_files_path
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def unstructured_path_rewrite(self, path):
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return "Rewrite<%s>" % path
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def test_dataset_false_extra_files_path():
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dataset = MockDataset()
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wrapper = DatasetFilenameWrapper(dataset)
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assert wrapper.extra_files_path == MOCK_DATASET_EXTRA_FILES_PATH
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new_path = "/new/path/dataset_123.dat"
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dataset_path = DatasetPath(123, MOCK_DATASET_PATH, false_path=new_path)
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wrapper = DatasetFilenameWrapper(dataset, compute_environment=MockComputeEnvironment(dataset_path))
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# Setting false_path is not enough to override
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assert wrapper.extra_files_path == MOCK_DATASET_EXTRA_FILES_PATH
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new_files_path = "/new/path/dataset_123_files"
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wrapper = DatasetFilenameWrapper(dataset, compute_environment=MockComputeEnvironment(false_path=new_path, false_extra_files_path=new_files_path))
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assert wrapper.extra_files_path == new_files_path
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def _drilldown_parameter(tool):
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xml = XML('''<param name="some_name" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true">
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<options>
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<option name="Heading 1" value="heading1">
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<option name="Option 1" value="option1"/>
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<option name="Option 2" value="option2"/>
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<option name="Heading 1" value="heading1">
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<option name="Option 3" value="option3"/>
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<option name="Option 4" value="option4"/>
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</option>
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</option>
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<option name="Option 5" value="option5"/>
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</options>
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</param>''')
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parameter = DrillDownSelectToolParameter(tool, xml)
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return parameter
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def _setup_blast_tool(tool, multiple=False):
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tool.app.write_test_tool_data("blastdb.loc", "val1\tname1\tpath1\nval2\tname2\tpath2\n")
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xml = XML('''<param name="database" type="select" label="Nucleotide BLAST database" multiple="%s">
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<options from_file="blastdb.loc">
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<column name="value" index="0"/>
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<column name="name" index="1"/>
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<column name="path" index="2"/>
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</options>
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</param>''' % multiple)
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parameter = SelectToolParameter(tool, xml)
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return parameter
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MOCK_DATASET_PATH = "/galaxy/database/files/001/dataset_123.dat"
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MOCK_DATASET_EXTRA_FILES_PATH = "/galaxy/database/files/001/dataset_123.dat"
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MOCK_DATASET_EXT = "bam"
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class MockDataset:
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def __init__(self):
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self.metadata = MetadataSpecCollection({})
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self.file_name = MOCK_DATASET_PATH
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self.extra_files_path = MOCK_DATASET_EXTRA_FILES_PATH
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self.ext = MOCK_DATASET_EXT
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self.tags = []
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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.options = Bunch(sanitize=False)
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class MockApp:
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def __init__(self, test_directory):
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self.config = Bunch(tool_data_path=test_directory)
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def write_test_tool_data(self, name, contents):
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path = os.path.join(self.config.tool_data_path, name)
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open(path, "w").write(contents)
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