def setUp(self):
self.setup_app()
self.tool = MockTool(self.app)
self.job = Job()
self.job.history = History()
self.job.parameters = [JobParameter(name="thresh", value="4")]
self.evaluator = ToolEvaluator(self.app, self.tool, self.job, self.test_directory)
def setUp(self):
self.setup_app()
self.tool = MockTool(self.app)
self.job = Job()
self.job.history = History()
self.job.parameters = [ JobParameter( name="thresh", value="4" ) ]
self.evaluator = ToolEvaluator( self.app, self.tool, self.job, self.test_directory )
class ToolEvaluatorTestCase(TestCase, UsesApp):
def setUp(self):
self.setup_app()
self.tool = MockTool(self.app)
self.job = Job()
self.job.history = History()
self.job.parameters = [JobParameter(name="thresh", value="4")]
self.evaluator = ToolEvaluator(self.app, self.tool, self.job,
self.test_directory)
def tearDown(self):
self.tear_down_app()
def test_simple_evaluation(self):
self._setup_test_bwa_job()
self._set_compute_environment()
command_line, extra_filenames = self.evaluator.build()
self.assertEquals(
command_line,
"bwa --thresh=4 --in=/galaxy/files/dataset_1.dat --out=/galaxy/files/dataset_2.dat"
)
def test_repeat_evaluation(self):
repeat = Repeat()
repeat.name = "r"
repeat.inputs = {"thresh": self.tool.test_thresh_param()}
self.tool.set_params({"r": repeat})
self.job.parameters = [
JobParameter(
name="r",
value=
'''[{"thresh": 4, "__index__": 0},{"thresh": 5, "__index__": 1}]'''
)
]
self.tool._command_line = "prog1 #for $r_i in $r # $r_i.thresh#end for#"
self._set_compute_environment()
command_line, extra_filenames = self.evaluator.build()
self.assertEquals(command_line, "prog1 4 5")
def test_conditional_evaluation(self):
select_xml = XML(
'''<param name="always_true" type="select"><option value="true">True</option></param>'''
)
parameter = SelectToolParameter(self.tool, select_xml)
conditional = Conditional()
conditional.name = "c"
conditional.test_param = parameter
when = ConditionalWhen()
when.inputs = {"thresh": self.tool.test_thresh_param()}
when.value = "true"
conditional.cases = [when]
self.tool.set_params({"c": conditional})
self.job.parameters = [
JobParameter(
name="c",
value=
'''{"thresh": 4, "always_true": "true", "__current_case__": 0}'''
)
]
self.tool._command_line = "prog1 --thresh=${c.thresh} --test_param=${c.always_true}"
self._set_compute_environment()
command_line, extra_filenames = self.evaluator.build()
self.assertEquals(command_line, "prog1 --thresh=4 --test_param=true")
def test_evaluation_of_optional_datasets(self):
# Make sure optional dataset don't cause evaluation to break and
# evaluate in cheetah templates as 'None'.
select_xml = XML(
'''<param name="input1" type="data" optional="true"></param>''')
parameter = DataToolParameter(self.tool, select_xml)
self.job.parameters = [JobParameter(name="input1", value=u'null')]
self.tool.set_params({"input1": parameter})
self.tool._command_line = "prog1 --opt_input='${input1}'"
self._set_compute_environment()
command_line, extra_filenames = self.evaluator.build()
self.assertEquals(command_line, "prog1 --opt_input='None'")
def test_evaluation_with_path_rewrites_wrapped(self):
self.tool.check_values = True
self.__test_evaluation_with_path_rewrites()
def test_evaluation_with_path_rewrites_unwrapped(self):
self.tool.check_values = False
self.__test_evaluation_with_path_rewrites()
def __test_evaluation_with_path_rewrites(self):
# Various things can cause dataset paths to be rewritten (Task
# splitting, config.outputs_to_working_directory). This tests that
#functionality.
self._setup_test_bwa_job()
job_path_1 = "%s/dataset_1.dat" % self.test_directory
job_path_2 = "%s/dataset_2.dat" % self.test_directory
self._set_compute_environment(
input_paths=[
DatasetPath(1,
'/galaxy/files/dataset_1.dat',
false_path=job_path_1)
],
output_paths=[
DatasetPath(2,
'/galaxy/files/dataset_2.dat',
false_path=job_path_2)
],
)
command_line, extra_filenames = self.evaluator.build()
self.assertEquals(
command_line,
"bwa --thresh=4 --in=%s --out=%s" % (job_path_1, job_path_2))
def test_configfiles_evaluation(self):
self.tool.config_files.append(("conf1", None, "$thresh"))
self.tool._command_line = "prog1 $conf1"
self._set_compute_environment()
command_line, extra_filenames = self.evaluator.build()
self.assertEquals(len(extra_filenames), 1)
config_filename = extra_filenames[0]
config_basename = os.path.basename(config_filename)
# Verify config file written into working directory.
self.assertEquals(os.path.join(self.test_directory, config_basename),
config_filename)
# Verify config file contents are evaluated against parameters.
assert open(config_filename, "r").read() == "4"
self.assertEquals(command_line, "prog1 %s" % config_filename)
def test_arbitrary_path_rewriting_wrapped(self):
self.tool.check_values = True
self.__test_arbitrary_path_rewriting()
def test_arbitrary_path_rewriting_unwrapped(self):
self.tool.check_values = False
self.__test_arbitrary_path_rewriting()
def __test_arbitrary_path_rewriting(self):
self.job.parameters = [
JobParameter(name="index_path", value="\"/old/path/human\"")
]
xml = XML('''<param name="index_path" type="select">
<option value="/old/path/human">Human</option>
<option value="/old/path/mouse">Mouse</option>
</param>''')
parameter = SelectToolParameter(self.tool, xml)
def get_field_by_name_for_value(name, value, trans, other_values):
assert value == "/old/path/human"
assert name == "path"
return ["/old/path/human"]
parameter.options = Bunch(
get_field_by_name_for_value=get_field_by_name_for_value)
self.tool.set_params({"index_path": parameter})
self.tool._command_line = "prog1 $index_path.fields.path"
def test_path_rewriter(v):
if v:
v = v.replace("/old", "/new")
return v
self._set_compute_environment(path_rewriter=test_path_rewriter)
command_line, extra_filenames = self.evaluator.build()
self.assertEquals(command_line, "prog1 /new/path/human")
def test_template_property_app(self):
self._assert_template_property_is("$__app__.config.new_file_path",
self.app.config.new_file_path)
def test_template_property_new_file_path(self):
self._assert_template_property_is("$__new_file_path__",
self.app.config.new_file_path)
def test_template_property_root_dir(self):
self._assert_template_property_is("$__root_dir__",
self.app.config.root)
def test_template_property_admin_users(self):
self._assert_template_property_is("$__admin_users__",
"*****@*****.**")
def _assert_template_property_is(self, expression, value):
self.tool._command_line = "test.exe"
self.tool.config_files.append(("conf1", None, """%s""" % expression))
self._set_compute_environment()
_, extra_filenames = self.evaluator.build()
config_filename = extra_filenames[0]
self.assertEquals(open(config_filename, "r").read(), value)
def _set_compute_environment(self, **kwds):
if "working_directory" not in kwds:
kwds["working_directory"] = self.test_directory
if "new_file_path" not in kwds:
kwds["new_file_path"] = self.app.config.new_file_path
self.evaluator.set_compute_environment(TestComputeEnviornment(**kwds))
assert "exec_before_job" in self.tool.hooks_called
def _setup_test_bwa_job(self):
self.job.input_datasets = [
self._job_dataset('input1', '/galaxy/files/dataset_1.dat')
]
self.job.output_datasets = [
self._job_dataset('output1', '/galaxy/files/dataset_2.dat')
]
def _job_dataset(self, name, path):
metadata = dict()
hda = HistoryDatasetAssociation(name=name, metadata=metadata)
hda.dataset = Dataset(id=123, external_filename=path)
hda.dataset.metadata = dict()
hda.children = []
jida = JobToInputDatasetAssociation(name=name, dataset=hda)
return jida
class ToolEvaluatorTestCase(TestCase, UsesApp):
def setUp(self):
self.setup_app()
self.tool = MockTool(self.app)
self.job = Job()
self.job.history = History()
self.job.parameters = [ JobParameter( name="thresh", value="4" ) ]
self.evaluator = ToolEvaluator( self.app, self.tool, self.job, self.test_directory )
def tearDown(self):
self.tear_down_app()
def test_simple_evaluation( self ):
self._setup_test_bwa_job()
self._set_compute_environment()
command_line, extra_filenames, _ = self.evaluator.build( )
self.assertEquals( command_line, "bwa --thresh=4 --in=/galaxy/files/dataset_1.dat --out=/galaxy/files/dataset_2.dat" )
def test_repeat_evaluation( self ):
repeat = Repeat()
repeat.name = "r"
repeat.inputs = { "thresh": self.tool.test_thresh_param() }
self.tool.set_params( { "r": repeat } )
self.job.parameters = [ JobParameter( name="r", value='''[{"thresh": 4, "__index__": 0},{"thresh": 5, "__index__": 1}]''' ) ]
self.tool._command_line = "prog1 #for $r_i in $r # $r_i.thresh#end for#"
self._set_compute_environment()
command_line, extra_filenames, _ = self.evaluator.build( )
self.assertEquals( command_line, "prog1 4 5" )
def test_conditional_evaluation( self ):
select_xml = XML('''<param name="always_true" type="select"><option value="true">True</option></param>''')
parameter = SelectToolParameter( self.tool, select_xml )
conditional = Conditional()
conditional.name = "c"
conditional.test_param = parameter
when = ConditionalWhen()
when.inputs = { "thresh": self.tool.test_thresh_param() }
when.value = "true"
conditional.cases = [ when ]
self.tool.set_params( { "c": conditional } )
self.job.parameters = [ JobParameter( name="c", value='''{"thresh": 4, "always_true": "true", "__current_case__": 0}''' ) ]
self.tool._command_line = "prog1 --thresh=${c.thresh} --test_param=${c.always_true}"
self._set_compute_environment()
command_line, extra_filenames, _ = self.evaluator.build( )
self.assertEquals( command_line, "prog1 --thresh=4 --test_param=true" )
def test_evaluation_of_optional_datasets( self ):
# Make sure optional dataset don't cause evaluation to break and
# evaluate in cheetah templates as 'None'.
select_xml = XML('''<param name="input1" type="data" optional="true"></param>''')
parameter = DataToolParameter( self.tool, select_xml )
self.job.parameters = [ JobParameter( name="input1", value=u'null' ) ]
self.tool.set_params( { "input1": parameter } )
self.tool._command_line = "prog1 --opt_input='${input1}'"
self._set_compute_environment()
command_line, extra_filenames, _ = self.evaluator.build( )
self.assertEquals( command_line, "prog1 --opt_input='None'" )
def test_evaluation_with_path_rewrites_wrapped( self ):
self.tool.check_values = True
self.__test_evaluation_with_path_rewrites()
def test_evaluation_with_path_rewrites_unwrapped( self ):
self.tool.check_values = False
self.__test_evaluation_with_path_rewrites()
def __test_evaluation_with_path_rewrites( self ):
# Various things can cause dataset paths to be rewritten (Task
# splitting, config.outputs_to_working_directory). This tests that
# functionality.
self._setup_test_bwa_job()
job_path_1 = "%s/dataset_1.dat" % self.test_directory
job_path_2 = "%s/dataset_2.dat" % self.test_directory
self._set_compute_environment(
input_paths=[DatasetPath(1, '/galaxy/files/dataset_1.dat', false_path=job_path_1)],
output_paths=[DatasetPath(2, '/galaxy/files/dataset_2.dat', false_path=job_path_2)],
)
command_line, extra_filenames, _ = self.evaluator.build( )
self.assertEquals( command_line, "bwa --thresh=4 --in=%s --out=%s" % (job_path_1, job_path_2) )
def test_configfiles_evaluation( self ):
self.tool.config_files.append( ( "conf1", None, "$thresh" ) )
self.tool._command_line = "prog1 $conf1"
self._set_compute_environment()
command_line, extra_filenames, _ = self.evaluator.build( )
self.assertEquals( len( extra_filenames ), 1)
config_filename = extra_filenames[ 0 ]
config_basename = os.path.basename( config_filename )
# Verify config file written into working directory.
self.assertEquals( os.path.join( self.test_directory, config_basename ), config_filename )
# Verify config file contents are evaluated against parameters.
assert open( config_filename, "r").read() == "4"
self.assertEquals(command_line, "prog1 %s" % config_filename)
def test_arbitrary_path_rewriting_wrapped( self ):
self.tool.check_values = True
self.__test_arbitrary_path_rewriting()
def test_arbitrary_path_rewriting_unwrapped( self ):
self.tool.check_values = False
self.__test_arbitrary_path_rewriting()
def __test_arbitrary_path_rewriting( self ):
self.job.parameters = [ JobParameter( name="index_path", value="\"/old/path/human\"" ) ]
xml = XML('''<param name="index_path" type="select">
<option value="/old/path/human">Human</option>
<option value="/old/path/mouse">Mouse</option>
</param>''')
parameter = SelectToolParameter( self.tool, xml )
def get_field_by_name_for_value( name, value, trans, other_values ):
assert value == "/old/path/human"
assert name == "path"
return ["/old/path/human"]
def get_options( trans, other_values ):
return [ [ "", "/old/path/human", "" ] ]
parameter.options = Bunch(get_field_by_name_for_value=get_field_by_name_for_value, get_options=get_options)
self.tool.set_params( {
"index_path": parameter
} )
self.tool._command_line = "prog1 $index_path.fields.path"
def test_path_rewriter(v):
if v:
v = v.replace("/old", "/new")
return v
self._set_compute_environment(path_rewriter=test_path_rewriter)
command_line, extra_filenames, _ = self.evaluator.build( )
self.assertEquals(command_line, "prog1 /new/path/human")
def test_template_property_app( self ):
self._assert_template_property_is("$__app__.config.new_file_path", self.app.config.new_file_path)
def test_template_property_new_file_path( self ):
self._assert_template_property_is("$__new_file_path__", self.app.config.new_file_path)
def test_template_property_root_dir( self ):
self._assert_template_property_is("$__root_dir__", self.app.config.root)
def test_template_property_admin_users( self ):
self._assert_template_property_is("$__admin_users__", "*****@*****.**")
def _assert_template_property_is(self, expression, value):
self.tool._command_line = "test.exe"
self.tool.config_files.append( ( "conf1", None, """%s""" % expression) )
self._set_compute_environment()
_, extra_filenames, _ = self.evaluator.build( )
config_filename = extra_filenames[ 0 ]
self.assertEquals(open( config_filename, "r").read(), value)
def _set_compute_environment(self, **kwds):
if "working_directory" not in kwds:
kwds[ "working_directory" ] = self.test_directory
if "new_file_path" not in kwds:
kwds[ "new_file_path" ] = self.app.config.new_file_path
self.evaluator.set_compute_environment( TestComputeEnviornment( **kwds ) )
assert "exec_before_job" in self.tool.hooks_called
def _setup_test_bwa_job( self ):
self.job.input_datasets = [ self._job_dataset( 'input1', '/galaxy/files/dataset_1.dat' ) ]
self.job.output_datasets = [ self._job_dataset( 'output1', '/galaxy/files/dataset_2.dat' ) ]
def _job_dataset( self, name, path ):
metadata = dict( )
hda = HistoryDatasetAssociation( name=name, metadata=metadata )
hda.dataset = Dataset( id=123, external_filename=path )
hda.dataset.metadata = dict()
hda.children = []
jida = JobToInputDatasetAssociation( name=name, dataset=hda )
return jida
