def test_strains_with_uri_and_trailing_strings(self):
ip_table = test_utils.create_fake_controls_table(1)
control_type = IntentParserCell()
control_type.add_paragraph('HIGH_FITC')
strains = IntentParserCell()
strains.add_paragraph(
'MG1655', link='https://hub.sd2e.org/user/sd2e/design/MG1655/1')
strains.add_paragraph(', MG1655_LPV3,MG1655_RPU_Standard')
data_row = test_utils.create_control_table_row(
strains_cell=strains, control_type_cell=control_type)
ip_table.add_row(data_row)
control_table_parser = ControlsTable(
ip_table,
strain_mapping=self.strain_mappings,
control_types={'HIGH_FITC'})
control_table_parser.process_table()
control_result = control_table_parser.get_intents()
self.assertEquals(1, len(control_result))
exp_res = {
'sbh_uri': 'https://hub.sd2e.org/user/sd2e/design/MG1655/1',
'label': 'strain1',
'lab_id': 'name.ip_admin.MG1655'
}
expected_result = {
dc_constants.TYPE: 'HIGH_FITC',
dc_constants.STRAINS: [exp_res]
}
self.assertEqual(expected_result,
control_result[0].to_structured_request())
def test_table_with_contents(self):
ip_table = test_utils.create_fake_controls_table(1)
control_type = IntentParserCell()
control_type.add_paragraph('HIGH_FITC')
content = IntentParserCell()
content.add_paragraph(
'beta_estradiol',
link='https://hub.sd2e.org/user/sd2e/design/beta_estradiol/1')
data_row = test_utils.create_control_table_row(
contents_cell=content, control_type_cell=control_type)
ip_table.add_row(data_row)
control_table_parser = ControlsTable(ip_table,
control_types={'HIGH_FITC'})
control_table_parser.process_table()
control_result = control_table_parser.get_intents()
content = {
dc_constants.NAME: {
dc_constants.LABEL:
'beta_estradiol',
dc_constants.SBH_URI:
'https://hub.sd2e.org/user/sd2e/design/beta_estradiol/1'
}
}
expected_result = {
dc_constants.TYPE: 'HIGH_FITC',
dc_constants.CONTENTS: [content]
}
self.assertEqual(expected_result,
control_result[0].to_structured_request())
def test_table_with_1_timepoint(self):
ip_table = test_utils.create_fake_controls_table(1)
content = IntentParserCell()
content.add_paragraph('8 hour')
control_type = IntentParserCell()
control_type.add_paragraph('HIGH_FITC')
data_row = test_utils.create_control_table_row(
timepoint_cell=content, control_type_cell=control_type)
ip_table.add_row(data_row)
control_table_parser = ControlsTable(ip_table,
timepoint_units={'hour'},
control_types={'HIGH_FITC'})
control_table_parser.process_table()
control_result = control_table_parser.get_intents()
self.assertEqual(1, len(control_result))
expected_timepoint = {
dc_constants.VALUE: 8.0,
dc_constants.UNIT: 'hour'
}
expected_result = {
dc_constants.TYPE: 'HIGH_FITC',
dc_constants.TIMEPOINTS: [expected_timepoint]
}
self.assertEqual(expected_result,
control_result[0].to_structured_request())
def test_table_with_control_type(self):
ip_table = test_utils.create_fake_controls_table(1)
control_type = IntentParserCell()
control_type.add_paragraph('HIGH_FITC')
data_row = test_utils.create_control_table_row(
control_type_cell=control_type)
ip_table.add_row(data_row)
control_table_parser = ControlsTable(ip_table,
control_types={'HIGH_FITC'})
control_table_parser.process_table()
control_result = control_table_parser.get_intents()
self.assertEqual(1, len(control_result))
expected_result = {dc_constants.TYPE: 'HIGH_FITC'}
self.assertEqual(expected_result,
control_result[0].to_structured_request())
def test_table_with_multiple_channels(self):
ip_table = test_utils.create_fake_controls_table(1)
control_type = IntentParserCell()
control_type.add_paragraph('HIGH_FITC')
channel = IntentParserCell()
channel.add_paragraph('BL1-A, BL2-A')
data_row = test_utils.create_control_table_row(
channel_cell=channel, control_type_cell=control_type)
ip_table.add_row(data_row)
control_table_parser = ControlsTable(ip_table,
control_types={'HIGH_FITC'})
control_table_parser.process_table()
control_result = control_table_parser.get_intents()
expected_result = {
dc_constants.TYPE: 'HIGH_FITC',
dc_constants.CHANNEL: 'BL1-A'
}
self.assertEqual(expected_result,
control_result[0].to_structured_request())