from unittest import TestCase
from galaxy.tools.parameters import basic
from galaxy.util import bunch
from xml.etree.ElementTree import XML
import tools_support
class BaseParameterTestCase( TestCase, tools_support.UsesApp ):
def setUp(self):
self.setup_app( mock_model=False )
self.mock_tool = bunch.Bunch(
app=self.app,
tool_type="default",
)
def _parameter_for(self, **kwds):
content = kwds["xml"]
param_xml = XML( content )
return basic.ToolParameter.build( self.mock_tool, param_xml )
class ParameterParsingTestCase( BaseParameterTestCase ):
""" Test the parsing of XML for most parameter types - in many
ways these are not very good tests since they break the abstraction
established by the tools. The docs tests in basic.py are better but
largely rely on HTML stuff we are moving to the client side so they
those tests may need to be updated anyway.
It occurs to me that rewriting this stuff to test to_dict would
be much better - since that is a public API of the the tools.
"""
def test_parse_help_and_label(self):
param = self._parameter_for(xml="""
""")
assert param.label == "x"
assert param.help == "y"
param = self._parameter_for(xml="""
y2
""")
assert param.label == "x2"
assert param.help == "y2"
def test_parse_sanitizers(self):
param = self._parameter_for(xml="""
""")
sanitizer = param.sanitizer
assert sanitizer is not None
assert sanitizer.sanitize_param("a") == ""
assert sanitizer.sanitize_param(",") == ","
def test_parse_optional(self):
param = self._parameter_for(xml="""
""")
assert param.optional is False
param = self._parameter_for(xml="""
""")
assert param.optional is True
def test_parse_validators(self):
param = self._parameter_for(xml="""
""")
assert param.validators[0].message == "no genome?"
def test_text_params(self):
param = self._parameter_for(xml="""
""")
assert param.size == "8"
assert param.value == "mydefault"
assert param.type == "text"
assert not param.area
def test_text_area_params(self):
param = self._parameter_for(xml="""
""")
assert param.size is None
assert param.value is None
assert param.type == "text"
assert param.area
def test_integer_params(self):
param = self._parameter_for(xml="""
""")
assert param.name == "intp"
assert param.value == "9"
assert param.type == "integer"
param.validate( 8 )
self.assertRaises(Exception, lambda: param.validate( 10 ))
def test_float_params(self):
param = self._parameter_for(xml="""
""")
assert param.name == "floatp"
assert param.value == "9"
assert param.type == "float"
param.validate( 8.1 )
self.assertRaises(Exception, lambda: param.validate( 10.0 ))
def test_boolean_params(self):
param = self._parameter_for(xml="""
""")
assert param.name == "boolp"
assert param.truevalue == "true"
assert param.falsevalue == "false"
assert param.type == "boolean"
param = self._parameter_for(xml="""
""")
assert param.truevalue == "t"
assert param.falsevalue == "f"
def test_file_params(self):
param = self._parameter_for(xml="""
""")
assert param.name == "filep"
assert param.type == "file"
assert param.ajax
def test_ftpfile_params(self):
param = self._parameter_for(xml="""
""")
assert param.name == "ftpfilep"
assert param.type == "ftpfile"
def test_hidden(self):
param = self._parameter_for(xml="""
""")
assert param.name == "hiddenp"
assert param.type == "hidden"
assert param.value == "a hidden value"
def test_base_url(self):
param = self._parameter_for(xml="""
""")
assert param.name == "urlp"
assert param.type == "baseurl"
assert param.value == "http://twitter.com/"
param = self._parameter_for(xml="""
""")
assert param.value == ""
def test_select_static(self):
param = self._parameter_for(xml="""
""")
assert param.display is None
assert param.multiple is True
assert param.name == "selectp"
assert param.type == "select"
assert param.separator == ","
assert param.options is None
assert param.dynamic_options is None
assert not param.is_dynamic
options = param.static_options
assert options[0][0] == "A"
assert options[0][1] == "a"
assert not options[0][2]
assert options[1][0] == "B"
assert options[1][1] == "b"
assert options[1][2]
def test_select_dynamic(self):
param = self._parameter_for(xml="""
""")
assert param.multiple is False
assert param.options is None
assert param.dynamic_options == "cow"
## This should be None or something - not undefined.
# assert not param.static_options
assert param.is_dynamic
assert param.display == "checkboxes"
assert param.separator == "moo"
def test_select_options_from(self):
param = self._parameter_for(xml="""
""")
assert param.dynamic_options is None
assert param.is_dynamic
# More detailed tests of dynamic options should be placed
# in test_select_parameters.
assert param.options.missing_tool_data_table_name == "cow"
def test_genome_build(self):
param = self._parameter_for(xml="""
""")
assert param.type == "genomebuild"
assert param.name == "genomep"
assert param.static_options
def test_column_params(self):
param = self._parameter_for(xml="""
""")
assert param.data_ref == "input1"
assert param.usecolnames is False
assert param.force_select is True
assert param.numerical is False
param = self._parameter_for(xml="""
""")
assert param.data_ref == "input1"
assert param.usecolnames is True
assert param.force_select is False
assert param.numerical is True
def test_data_param_no_validation(self):
param = self._parameter_for(xml="""
""")
assert len(param.validators) == 1
param = self._parameter_for(xml="""
""")
assert len(param.validators) == 0
def test_data_param_dynamic_options(self):
param = self._parameter_for(xml="""
""")
assert param.options is None
assert param.options_filter_attribute is None
param = self._parameter_for(xml="""
""")
assert param.options is not None
assert param.options_filter_attribute is None
param = self._parameter_for(xml="""
""")
assert param.options is not None
assert param.options_filter_attribute == "cow"
def test_conversions(self):
param = self._parameter_for(xml="""
""")
assert param.conversions == []
param = self._parameter_for(xml="""
""")
assert param.conversions[0][0] == "foo"
assert param.conversions[0][1] == "txt"
assert param.conversions[1][0] == "foo2"
assert param.conversions[1][1] == "bam"
def test_drilldown(self):
param = self._parameter_for(xml="""
""")
assert param.type == "drill_down"
assert param.name == "some_name"
assert param.options
heading1 = param.options[0]
assert heading1["selected"] is False
assert heading1["name"] == "Heading 1"
assert heading1["value"] == "heading1"
option1 = heading1["options"][0]
assert option1["selected"] is False
assert option1["name"] == "Option 1"
assert option1["value"] == "option1"
option5 = param.options[1]
assert option5["selected"] is False
assert option5["name"] == "Option 5"
assert option5["value"] == "option5"
assert len(option5["options"]) == 0
def test_tool_collection(self):
param = self._parameter_for(xml="""
""")
assert param.type == "data_collection"
assert param.collection_type == "list"
def test_library(self):
param = self._parameter_for(xml="""
""")
assert param.type == "library_data"
assert param.name == "libraryp"