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95 lines
4.4 KiB
Python
95 lines
4.4 KiB
Python
import sys
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import new
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from base.twilltestcase import TwillTestCase
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toolbox = None
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class ToolTestCase( TwillTestCase ):
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"""Abstract test case that runs tests based on a `galaxy.tools.test.ToolTest`"""
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def do_it( self ):
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# If the test generation had an error, raise
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if self.testdef.error:
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if self.testdef.exception:
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raise self.testdef.exception
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else:
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raise Exception( "Test parse failure" )
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# Start with a new history
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self.login()
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if len(self.get_history()) > 0:
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raise AssertionError("ToolTestCase.do_it failed")
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# Upload any needed files
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for fname, extra in self.testdef.required_files:
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self.upload_file( fname, ftype=extra.get( 'ftype', 'auto' ), dbkey=extra.get( 'dbkey', 'hg17' ) )
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print fname, extra
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# Run the tool
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all_inputs = dict( ( name, value ) for ( name, value, _ ) in self.testdef.inputs )
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# Do the first page
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page_inputs = self.__expand_grouping(self.testdef.tool.inputs_by_page[0], all_inputs)
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self.run_tool( self.testdef.tool.id, **page_inputs )
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print "page_inputs (0)", page_inputs
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# Do other pages if they exist
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for i in range( 1, self.testdef.tool.npages ):
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page_inputs = self.__expand_grouping(self.testdef.tool.inputs_by_page[i], all_inputs)
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self.submit_form( **page_inputs )
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print "page_inputs (%i)" % i, page_inputs
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# Check the result
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assert len( self.testdef.outputs ) == 1, "ToolTestCase does not deal with multiple outputs properly yet."
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for name, file in self.testdef.outputs:
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self.verify_dataset_correctness( file )
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#Clean up
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self.delete_history()
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self.logout()
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def shortDescription( self ):
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return self.name
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def __expand_grouping(self, tool_inputs, declared_inputs ):
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expanded_inputs = {}
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for key, value in tool_inputs.items():
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import galaxy.tools.grouping
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if isinstance(value, galaxy.tools.grouping.Conditional):
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for i, case in enumerate(value.cases):
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if declared_inputs[value.test_param.name] == case.value:
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if isinstance(case.value, str):
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expanded_inputs["%s|%s" % (value.name, value.test_param.name)] = case.value.split(",")
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else:
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expanded_inputs["%s|%s" % (value.name, value.test_param.name)] = case.value
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for input_name, input_value in case.inputs.items():
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if isinstance(input_value, galaxy.tools.grouping.Conditional):
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expanded_inputs.update(self.__expand_grouping({input_name:input_value}), declared_inputs)
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elif isinstance(declared_inputs[input_name], str):
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expanded_inputs.update({"%s|%s" % (value.name, input_name):declared_inputs[input_name].split(",")})
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else:
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expanded_inputs.update({"%s|%s" % (value.name, input_name):declared_inputs[input_name]})
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elif isinstance(declared_inputs[value.name], str):
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expanded_inputs[value.name] = declared_inputs[value.name].split(",")
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else:
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expanded_inputs[value.name] = declared_inputs[value.name]
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return expanded_inputs
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def get_testcase( testdef, name ):
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"""Dynamically generate a `ToolTestCase` for `testdef`"""
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n = "TestForTool_" + testdef.tool.id.replace( ' ', '_' )
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s = ( ToolTestCase, )
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def test_tool( self ):
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self.do_it()
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d = dict( testdef=testdef, test_tool=test_tool, name=name )
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return new.classobj( n, s, d )
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def setup():
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"""
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If the module level variable `toolbox` is set, generate `ToolTestCase`
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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 toolbox is None:
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return
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# Push all the toolbox tests to module level
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G = globals()
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for i, section in enumerate( toolbox.sections ):
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for j, tool in enumerate( section.tools ):
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if tool.tests:
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for k, testdef in enumerate( tool.tests ):
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name = "%s > %s > %s" % ( section.name, tool.name, testdef.name )
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testcase = get_testcase( testdef, name )
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G[ 'testcase_%d_%d_%d' % ( i, j, k ) ] = testcase
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