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_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 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 __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"
self._set_compute_environment(
unstructured_path_rewrites={"/old": "/new"})
command_line = self.evaluator.build()[0]
self.assertEqual(command_line, "prog1 /new/path/human")
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 # $r_i.thresh#end for#"
self._set_compute_environment()
command_line, extra_filenames, _ = self.evaluator.build()
self.assertEqual(command_line, "prog1 4 5")
def test_evaluation_of_optional_datasets(self):
# Make sure optional dataset don't cause evaluation to break and
# evaluate in cheetah templates as 'None'.
select_xml = XML('''<param name="input1" type="data" optional="true"></param>''')
parameter = DataToolParameter(self.tool, select_xml)
self.job.parameters = [JobParameter(name="input1", value=u'null')]
self.tool.set_params({"input1": parameter})
self.tool._command_line = "prog1 --opt_input='${input1}'"
self._set_compute_environment()
command_line, extra_filenames, _ = self.evaluator.build()
self.assertEqual(command_line, "prog1 --opt_input='None'")
