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https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 02:04:04 +08:00
James Taylor
7bfc238304
#) An "xy_plot" tool and a new "build_ucsc_custom_track" tool that
demonstrate the various features added here.
#) Grouping constructs for tool parameters:
- "repeat" element allows for a set of parameters to be repeated an
arbitrary number of times
- "conditional" element allows choosing a set of parameters to display
based on the value of another parameter
These constructs can be arbitrarily nested. Their values are structured
and can be used in hooks, validation, et cetera
#) Support for generating arbitrary config files to pass to a tool
#) Command lines are now full Cheetah templates
#) Better job error reporting, includes tracebacks for internal errors
preparing the job (database change required, see below!)
#) Preparation of command line, config files, exec_before_job hook moved
into job execution stage
#) Parameter values now jsonified before storing in database (this is much
more rigorous that before, and restoring from the database now works
properly)
DATABASE CHANGE:
alter table job add column traceback text;
69 lines
2.7 KiB
Python
69 lines
2.7 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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"""
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Abstract test case that runs tests based on a `galaxy.tools.test.ToolTest`
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"""
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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 an empty history
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self.clear_history()
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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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# 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 = dict( ( key, all_inputs[key] )
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for key in self.testdef.tool.inputs_by_page[0].keys() )
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self.run_tool( self.testdef.tool.id, **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 = dict( ( key, all_inputs[key] )
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for key in self.testdef.tool.inputs_by_page[i].keys() )
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self.submit_form( **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.check_data( file )
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def shortDescription( self ):
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return self.name
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def get_testcase( testdef, name ):
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"""
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Dynamically generate a `ToolTestCase` for `testdef`
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"""
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n = "GeneratedToolTestCase_" + 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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