mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-13 00:44:55 +08:00
John Chilton
cddd727c05
Slightly confusing that state params and raw incoming passed to that method, so pull out rerun_remap_job_id sooner and just pass that along (it was the only incoming was used for). Use the oppertunity to isolate potential errors with decoding rerun_remap_job_id and include more informative error message. Add unit test to test invalid rerun_remap_job_ids.
259 lines
9.3 KiB
Python
259 lines
9.3 KiB
Python
""" Test Tool execution and state handling logic.
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"""
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import os
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from unittest import TestCase
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import galaxy.model
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from galaxy.tools import Tool
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from galaxy.tools import DefaultToolState
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from galaxy.tools.parameters import params_to_incoming
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from galaxy.util import parse_xml
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from galaxy.util.bunch import Bunch
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from galaxy.util import string_to_object
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from galaxy.util import object_to_string
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from galaxy.util.odict import odict
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from tools_support import UsesApp
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# Simple tool with just one text parameter and output.
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SIMPLE_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool">
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<command>echo "$param1" < $out1</command>
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<inputs>
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<param type="text" name="param1" value="" />
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</inputs>
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<outputs>
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<output name="out1" format="data" />
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</outputs>
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</tool>'''
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# Tool with a repeat parameter, to test state update.
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REPEAT_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool">
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<command>echo "$param1" #for $r in $repeat# "$r.param2" #end for# < $out1</command>
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<inputs>
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<param type="text" name="param1" value="" />
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<repeat name="repeat1" label="Repeat 1">
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<param type="text" name="param2" value="" />
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</repeat>
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</inputs>
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<outputs>
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<output name="out1" format="data" />
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</outputs>
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</tool>
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'''
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# A tool with data parameters (kind of like cat1) my favorite test tool :)
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SIMPLE_CAT_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool">
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<command>cat "$param1" #for $r in $repeat# "$r.param2" #end for# < $out1</command>
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<inputs>
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<param type="data" format="tabular" name="param1" value="" />
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<repeat name="repeat1" label="Repeat 1">
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<param type="data" format="tabular" name="param2" value="" />
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</repeat>
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</inputs>
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<outputs>
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<output name="out1" format="data" />
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</outputs>
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</tool>
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'''
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class ToolExecutionTestCase( TestCase, UsesApp ):
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def setUp(self):
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self.setup_app()
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self.history = galaxy.model.History()
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self.app.job_config["get_job_tool_configurations"] = lambda ids: None
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self.app.config.drmaa_external_runjob_script = ""
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self.app.config.tool_secret = "testsecret"
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self.trans = MockTrans( self.app, self.history )
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self.tool_action = MockAction( self.trans )
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self.tool_file = os.path.join( self.test_directory, "tool.xml" )
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def tearDown(self):
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self.tear_down_app()
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def test_state_new( self ):
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self.__init_tool( SIMPLE_TOOL_CONTENTS )
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template, template_vars = self.__handle_with_incoming(
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param1="moo",
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# no runtool_btn, just rerenders the form mako with tool
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# state populated.
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)
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state = self.__assert_rerenders_tool_without_errors( template, template_vars )
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assert state.inputs[ "param1" ] == "moo"
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def test_execute( self ):
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self.__init_tool( SIMPLE_TOOL_CONTENTS )
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template, template_vars = self.__handle_with_incoming(
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param1="moo",
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runtool_btn="dummy",
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)
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assert template == "tool_executed.mako"
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# Didn't specify a rerun_remap_id so this should be None
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assert self.tool_action.execution_call_args[ 0 ][ "rerun_remap_job_id" ] is None
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def test_remap_job( self ):
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self.__init_tool( SIMPLE_TOOL_CONTENTS )
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template, template_vars = self.__handle_with_incoming(
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param1="moo",
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rerun_remap_job_id=self.app.security.encode_id(123),
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runtool_btn="dummy",
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)
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assert template == "tool_executed.mako"
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assert self.tool_action.execution_call_args[ 0 ][ "rerun_remap_job_id" ] == 123
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def test_invalid_remap_job( self ):
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self.__init_tool( SIMPLE_TOOL_CONTENTS )
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template, template_vars = self.__handle_with_incoming(
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param1="moo",
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rerun_remap_job_id='123', # Not encoded
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runtool_btn="dummy",
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)
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assert template == "message.mako"
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assert template_vars[ "status" ] == "error"
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assert "invalid job" in template_vars[ "message" ]
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def test_repeat_state_updates( self ):
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self.__init_tool( REPEAT_TOOL_CONTENTS )
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# Fresh state contains no repeat elements
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template, template_vars = self.__handle_with_incoming()
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state = self.__assert_rerenders_tool_without_errors( template, template_vars )
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assert len( state.inputs[ "repeat1" ] ) == 0
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# Hitting add button adds repeat element
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template, template_vars = self.__handle_with_incoming(
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repeat1_add="dummy",
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)
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state = self.__assert_rerenders_tool_without_errors( template, template_vars )
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assert len( state.inputs[ "repeat1" ] ) == 1
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# Hitting add button again adds another repeat element
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template, template_vars = self.__handle_with_incoming( state, **{
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"repeat1_add": "dummy",
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"repeat1_0|param2": "moo2",
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} )
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state = self.__assert_rerenders_tool_without_errors( template, template_vars )
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assert len( state.inputs[ "repeat1" ] ) == 2
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assert state.inputs[ "repeat1" ][ 0 ][ "param2" ] == "moo2"
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# Hitting remove drops a repeat element
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template, template_vars = self.__handle_with_incoming( state, repeat1_1_remove="dummy" )
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state = self.__assert_rerenders_tool_without_errors( template, template_vars )
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assert len( state.inputs[ "repeat1" ] ) == 1
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def test_data_param_execute( self ):
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self.__init_tool( SIMPLE_CAT_TOOL_CONTENTS )
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hda = self.__add_dataset(1)
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# Execute tool action
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template, template_vars = self.__handle_with_incoming(
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param1=1,
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runtool_btn="dummy",
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)
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assert template == "tool_executed.mako"
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# Tool 'executed' once, with hda as param1
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assert len( self.tool_action.execution_call_args ) == 1
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assert self.tool_action.execution_call_args[ 0 ][ "incoming" ][ "param1" ] == hda
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def test_data_param_state_update( self ):
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self.__init_tool( SIMPLE_CAT_TOOL_CONTENTS )
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hda = self.__add_dataset( 1 )
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# Update state
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template, template_vars = self.__handle_with_incoming(
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param1=1,
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)
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state = self.__assert_rerenders_tool_without_errors( template, template_vars )
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assert hda == state.inputs[ "param1" ]
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def __handle_with_incoming( self, previous_state=None, **kwds ):
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""" Execute tool.handle_input with incoming specified by kwds
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(optionally extending a previous state).
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"""
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if previous_state:
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incoming = self.__to_incoming( previous_state, **kwds)
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else:
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incoming = kwds
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return self.tool.handle_input(
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trans=self.trans,
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incoming=incoming,
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)
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def __to_incoming( self, state, **kwds ):
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new_incoming = {}
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params_to_incoming( new_incoming, self.tool.inputs, state.inputs, self.app )
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new_incoming[ "tool_state" ] = self.__state_to_string( state )
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new_incoming.update( kwds )
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return new_incoming
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def __add_dataset( self, id, state='ok' ):
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hda = galaxy.model.HistoryDatasetAssociation()
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hda.id = id
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hda.dataset = galaxy.model.Dataset()
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hda.dataset.state = 'ok'
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self.trans.sa_session.model_objects[ galaxy.model.HistoryDatasetAssociation ][ id ] = hda
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self.history.datasets.append( hda )
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return hda
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def __assert_rerenders_tool_without_errors( self, template, template_vars ):
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assert template == "tool_form.mako"
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assert not template_vars[ "errors" ]
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state = template_vars[ "tool_state" ]
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return state
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def __init_tool( self, tool_contents ):
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self.__write_tool( tool_contents )
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self.__setup_tool( )
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def __setup_tool( self ):
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tree = parse_xml( self.tool_file )
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self.tool = Tool( self.tool_file, tree.getroot(), self.app )
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self.tool.tool_action = self.tool_action
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def __write_tool( self, contents ):
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open( self.tool_file, "w" ).write( contents )
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def __string_to_state( self, state_string ):
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encoded_state = string_to_object( state_string )
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state = DefaultToolState()
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state.decode( encoded_state, self.tool, self.app )
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return state
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def __inputs_to_state( self, inputs ):
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tool_state = DefaultToolState()
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tool_state.inputs = inputs
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return tool_state
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def __state_to_string( self, tool_state ):
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return object_to_string( tool_state.encode( self.tool, self.app ) )
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def __inputs_to_state_string( self, inputs ):
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tool_state = self.__inputs_to_state( inputs )
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return self.__state_to_string( tool_state )
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class MockAction( object ):
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def __init__( self, expected_trans ):
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self.expected_trans = expected_trans
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self.execution_call_args = []
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def execute( self, tool, trans, **kwds ):
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assert self.expected_trans == trans
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self.execution_call_args.append( kwds )
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return None, odict(dict(out1="1"))
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class MockTrans( object ):
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def __init__( self, app, history ):
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self.app = app
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self.history = history
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self.history = galaxy.model.History()
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self.workflow_building_mode = False
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self.webapp = Bunch( name="galaxy" )
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self.sa_session = self.app.model.context
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def get_history( self ):
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return self.history
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