def test_measurement_with_neg_control_content_size_1(self):
measurement_intent = MeasurementIntent()
measurement_intent.set_measurement_type(
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE)
measurement_intent.add_file_type('SPREADSHEET')
content = ContentIntent()
num_neg_control = NamedIntegerValue(
NamedLink(ip_constants.HEADER_NUMBER_OF_NEGATIVE_CONTROLS_VALUE),
2)
content.set_numbers_of_negative_controls([num_neg_control])
measurement_intent.add_content(content)
content_structure_request = [{
dc_constants.NAME: {
dc_constants.LABEL:
ip_constants.HEADER_NUMBER_OF_NEGATIVE_CONTROLS_VALUE,
dc_constants.SBH_URI: dc_constants.NO_PROGRAM_DICTIONARY
},
dc_constants.VALUE: 2
}]
self.assertDictEqual(
{
dc_constants.CONTENTS: [content_structure_request],
dc_constants.FILE_TYPE: ['SPREADSHEET'],
dc_constants.MEASUREMENT_TYPE:
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE
}, measurement_intent.to_structured_request())
def test_measurement_with_strain_size_1(self):
measurement_intent = MeasurementIntent()
measurement_intent.set_measurement_type(
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE)
measurement_intent.add_file_type('SPREADSHEET')
strain_name = NamedLink('and_00',
link='www.synbiohub.org/example/strain')
strain = StrainIntent(strain_name)
strain.set_strain_lab_name('my_lab')
strain.set_strain_common_name('my_strain')
measurement_intent.add_strain(strain)
strain_structure_request = {
dc_constants.SBH_URI: 'www.synbiohub.org/example/strain',
dc_constants.LABEL: 'my_strain',
dc_constants.LAB_ID: 'name.my_lab.and_00'
}
self.assertEqual(
{
dc_constants.MEASUREMENT_TYPE:
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE,
dc_constants.FILE_TYPE: ['SPREADSHEET'],
dc_constants.STRAINS: [strain_structure_request]
}, measurement_intent.to_structured_request())
def test_measurement_with_file_type_and_measurement_type(self):
measurement_intent = MeasurementIntent()
measurement_intent.set_measurement_type(
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE)
measurement_intent.add_file_type('SPREADSHEET')
self.assertEqual(
{
dc_constants.MEASUREMENT_TYPE:
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE,
dc_constants.FILE_TYPE: ['SPREADSHEET']
}, measurement_intent.to_structured_request())
def test_measurement_with_ods_size_1(self):
measurement_intent = MeasurementIntent()
measurement_intent.set_measurement_type(
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE)
measurement_intent.add_file_type('SPREADSHEET')
measurement_intent.add_optical_density(3.0)
self.assertEqual(
{
dc_constants.MEASUREMENT_TYPE:
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE,
dc_constants.FILE_TYPE: ['SPREADSHEET'],
dc_constants.ODS: [3.0]
}, measurement_intent.to_structured_request())
def test_measurement_with_replicate_size_1(self):
measurement_intent = MeasurementIntent()
measurement_intent.set_measurement_type(
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE)
measurement_intent.add_file_type('SPREADSHEET')
measurement_intent.add_replicate(5)
self.assertEqual(
{
dc_constants.MEASUREMENT_TYPE:
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE,
dc_constants.FILE_TYPE: ['SPREADSHEET'],
dc_constants.REPLICATES: [5]
}, measurement_intent.to_structured_request())
def test_measurement_with_control_type(self):
measurement_intent = MeasurementIntent()
measurement_intent.set_measurement_type(
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE)
measurement_intent.add_file_type('SPREADSHEET')
control = ControlIntent()
control.set_control_type('HIGH_FITC')
measurement_intent.add_control(control)
control_structure_request = {dc_constants.TYPE: 'HIGH_FITC'}
self.assertEqual(
{
dc_constants.MEASUREMENT_TYPE:
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE,
dc_constants.FILE_TYPE: ['SPREADSHEET'],
dc_constants.CONTROLS: [control_structure_request]
}, measurement_intent.to_structured_request())
def test_measurement_with_temperature_size_1(self):
measurement_intent = MeasurementIntent()
measurement_intent.set_measurement_type(
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE)
measurement_intent.add_file_type('SPREADSHEET')
temperature = TemperatureIntent(75.0, 'fahrenheit')
measurement_intent.add_temperature(temperature)
temperature_structure_request = {
dc_constants.VALUE: 75.0,
dc_constants.UNIT: 'fahrenheit'
}
self.assertEqual(
{
dc_constants.MEASUREMENT_TYPE:
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE,
dc_constants.FILE_TYPE: ['SPREADSHEET'],
dc_constants.TEMPERATURES: [temperature_structure_request]
}, measurement_intent.to_structured_request())
def test_measurement_with_timepoint_size_1(self):
measurement_intent = MeasurementIntent()
measurement_intent.set_measurement_type(
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE)
measurement_intent.add_file_type('SPREADSHEET')
timepoint = TimepointIntent(12.0, 'hour')
measurement_intent.add_timepoint(timepoint)
timepoint_structure_request = {
dc_constants.VALUE: 12.0,
dc_constants.UNIT: 'hour'
}
self.assertEqual(
{
dc_constants.MEASUREMENT_TYPE:
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE,
dc_constants.FILE_TYPE: ['SPREADSHEET'],
dc_constants.TIMEPOINTS: [timepoint_structure_request]
}, measurement_intent.to_structured_request())
def test_measurement_with_strain_size_2(self):
measurement_intent = MeasurementIntent()
measurement_intent.set_measurement_type(
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE)
measurement_intent.add_file_type('SPREADSHEET')
strain_value1 = NamedLink('and_00',
link='www.synbiohub.org/example/and_strain')
strain1 = StrainIntent(strain_value1)
strain1.set_strain_lab_name('my_lab')
strain1.set_strain_common_name('and_strain')
measurement_intent.add_strain(strain1)
strain_value2 = NamedLink('or_gate',
link='www.synbiohub.org/example/or_strain')
strain2 = StrainIntent(strain_value2)
strain2.set_strain_lab_name('my_lab')
strain2.set_strain_common_name('or_strain')
measurement_intent.add_strain(strain2)
strain_structure_request = [{
dc_constants.SBH_URI: 'www.synbiohub.org/example/and_strain',
dc_constants.LABEL: 'and_strain',
dc_constants.LAB_ID: 'name.my_lab.and_00'
}, {
dc_constants.SBH_URI: 'www.synbiohub.org/example/or_strain',
dc_constants.LABEL: 'or_strain',
dc_constants.LAB_ID: 'name.my_lab.or_gate'
}]
self.assertEqual(
{
dc_constants.MEASUREMENT_TYPE:
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE,
dc_constants.FILE_TYPE: ['SPREADSHEET'],
dc_constants.STRAINS: strain_structure_request
}, measurement_intent.to_structured_request())
def test_measurement_with_missing_measurement_type(self):
measurement_intent = MeasurementIntent()
measurement_intent.add_file_type('SPREADSHEET')
with self.assertRaises(IntentParserException):
measurement_intent.to_structured_request()