mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Nicola Soranzo
21b44bf348
using the following command: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 . ```
113 lines
4.8 KiB
Python
113 lines
4.8 KiB
Python
import logging
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import new
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import os.path
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import shutil
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import tempfile
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from base.interactor import stage_data_in_history
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from .test_toolbox import ToolTestCase
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log = logging.getLogger(__name__)
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data_managers = None
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class DataManagerToolTestCase(ToolTestCase):
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"""Test case that runs Data Manager tests based on a `galaxy.tools.test.ToolTest`"""
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def do_it(self, testdef):
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"""
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Run through a tool test case.
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"""
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shed_tool_id = self.shed_tool_id
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self._handle_test_def_errors(testdef)
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galaxy_interactor = self._galaxy_interactor(testdef)
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test_history = galaxy_interactor.new_history() # history where inputs will be put, if any
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stage_data_in_history(galaxy_interactor, testdef.test_data(), test_history, shed_tool_id)
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galaxy_interactor.run_tool(testdef, test_history) # test_history will have inputs only, outputs are placed in the specialized data manager history
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# FIXME: Move history determination and switching into the interactor
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data_manager_history = None
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for assoc in reversed(test_history.user.data_manager_histories):
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if not assoc.history.deleted:
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data_manager_history = assoc.history
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break
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self.switch_history(id=self.security.encode_id(data_manager_history.id))
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data_list = self.get_history_as_data_list()
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# end
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self.assertTrue(data_list)
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self._verify_outputs(testdef, data_manager_history, shed_tool_id, data_list, galaxy_interactor)
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self.switch_history(id=self.security.encode_id(test_history.id))
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galaxy_interactor.delete_history(test_history)
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def build_tests(tmp_dir=None, testing_shed_tools=False, master_api_key=None, user_api_key=None):
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"""
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If the module level variable `data_managers` is set, generate `DataManagerToolTestCase`
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classes for all of its tests and put them into this modules globals() so
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they can be discovered by nose.
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"""
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if data_managers is None:
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log.warning('data_managers was not set for Data Manager functional testing. Will not test.')
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return
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# Push all the data_managers tests to module level
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G = globals()
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# Eliminate all previous tests from G.
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for key, val in G.items():
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if key.startswith('TestForDataManagerTool_'):
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del G[key]
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# first we will loop through data table loc files and copy them to temporary location, then swap out filenames:
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for data_table_name, data_table in data_managers.app.tool_data_tables.get_tables().items():
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for filename, value in list(data_table.filenames.items()):
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new_filename = tempfile.NamedTemporaryFile(prefix=os.path.basename(filename), dir=tmp_dir).name
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try:
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shutil.copy(filename, new_filename)
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except IOError as e:
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log.warning("Failed to copy '%s' to '%s', will create empty file at '%s': %s", filename, new_filename, new_filename, e)
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open(new_filename, 'wb').close()
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if 'filename' in value:
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value['filename'] = new_filename
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del data_table.filenames[filename] # remove filename:value pair
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data_table.filenames[new_filename] = value # add new value by
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for i, (data_manager_id, data_manager) in enumerate(data_managers.data_managers.items()):
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tool = data_manager.tool
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if not tool:
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log.warning("No Tool has been specified for Data Manager: %s", data_manager_id)
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if tool.tests:
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# fixme data_manager.tool_shed_repository_info_dict should be filled when is toolshed based
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shed_tool_id = None if not testing_shed_tools else tool.id
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# Create a new subclass of ToolTestCase, dynamically adding methods
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# named test_tool_XXX that run each test defined in the tool config.
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name = "TestForDataManagerTool_" + data_manager_id.replace(' ', '_')
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baseclasses = (DataManagerToolTestCase, )
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namespace = dict()
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for j, testdef in enumerate(tool.tests):
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def make_test_method(td):
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def test_tool(self):
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self.do_it(td)
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return test_tool
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test_method = make_test_method(testdef)
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test_method.__doc__ = "%s ( %s ) > %s" % (tool.name, tool.id, testdef.name)
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namespace['test_tool_%06d' % j] = test_method
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namespace['shed_tool_id'] = shed_tool_id
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namespace['master_api_key'] = master_api_key
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namespace['user_api_key'] = user_api_key
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# The new.classobj function returns a new class object, with name name, derived
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# from baseclasses (which should be a tuple of classes) and with namespace dict.
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new_class_obj = new.classobj(name, baseclasses, namespace)
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G[name] = new_class_obj
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