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_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_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 $index_path.fields.path"
self._set_compute_environment(
unstructured_path_rewrites={"/old": "/new"})
command_line = self.evaluator.build()[0]
self.assertEqual(command_line, "prog1 /new/path/human")
def test_conditional_evaluation(self):
select_xml = XML(
'''<param name="always_true" type="select"><option value="true">True</option></param>'''
)
parameter = SelectToolParameter(self.tool, select_xml)
conditional = Conditional()
conditional.name = "c"
conditional.test_param = parameter
when = ConditionalWhen()
when.inputs = {"thresh": self.tool.test_thresh_param()}
when.value = "true"
conditional.cases = [when]
self.tool.set_params({"c": conditional})
self.job.parameters = [
JobParameter(
name="c",
value=
'''{"thresh": 4, "always_true": "true", "__current_case__": 0}'''
)
]
self.tool._command_line = "prog1 --thresh=${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 selectwrapper(tool, value, multiple=False, optional=False):
optional = 'optional="true"' if optional else ''
multiple = 'multiple="true"' if multiple else ''
xml = XML('''<param name="blah" type="select" %s %s>
<option value="x">I am X</option>
<option value="y" selected="true">I am Y</option>
<option value="z">I am Z</option>
</param>''' % (multiple, optional))
parameter = SelectToolParameter(tool, xml)
return SelectToolParameterWrapper(parameter, value)
def test_select_wrapper_simple_options(tool):
xml = XML('''<param name="blah" type="select">
<option value="x">I am X</option>
<option value="y" selected="true">I am Y</option>
<option value="z">I am Z</option>
</param>''')
parameter = SelectToolParameter(tool, xml)
wrapper = SelectToolParameterWrapper(parameter, "x", tool.app)
assert str(wrapper) == "x"
assert wrapper.name == "blah"
assert wrapper.value_label == "I am X"
def _setup_blast_tool(tool, multiple=False):
tool.app.write_test_tool_data("blastdb.loc", "val1\tname1\tpath1\nval2\tname2\tpath2\n")
xml = XML('''<param name="database" type="select" label="Nucleotide BLAST database" multiple="%s">
<options from_file="blastdb.loc">
<column name="value" index="0"/>
<column name="name" index="1"/>
<column name="path" index="2"/>
</options>
</param>''' % multiple)
parameter = SelectToolParameter(tool, xml)
return parameter
def get_inputs( self ):
# TODO: Use an external xml or yaml file to load the parameter definition
parameter_type = self.state.inputs.get( "parameter_type", self.default_parameter_type )
optional = self.state.inputs.get( "optional", self.default_optional )
input_parameter_type = SelectToolParameter( None, XML(
'''
<param name="parameter_type" label="Parameter type" type="select" value="%s">
<option value="text">Text</option>
<option value="integer">Integer</option>
<option value="float">Float</option>
<option value="boolean">Boolean (True or False)</option>
<option value="color">Color</option>
</param>
''' % parameter_type ) )
return odict([( "parameter_type", input_parameter_type ),
( "optional", BooleanToolParameter( None, Element( "param", name="optional", label="Optional", type="boolean", value=optional )))])
def test_select_wrapper_multiple_options(tool):
xml = XML('''<param name="blah" type="select" multiple="true">
<option value="x">I am X</option>
<option value="y" selected="true">I am Y</option>
<option value="z">I am Z</option>
</param>''')
parameter = SelectToolParameter(tool, xml)
wrapper = SelectToolParameterWrapper(parameter, ["x"])
assert wrapper.name == "blah"
assert str(wrapper) == "x"
assert "x" in wrapper
wrapper = SelectToolParameterWrapper(parameter, ["x", "z"])
assert str(wrapper) == "x,z"
assert "x" in wrapper
wrapper = SelectToolParameterWrapper(parameter, [])
assert str(wrapper) == "None"
assert "x" not in wrapper