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_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_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_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_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 _process_protocol_measurement_type(self, measurement_types):
for opil_measurement_type in measurement_types:
measurement_intent = MeasurementIntent()
if opil_measurement_type.type == ip_constants.NCIT_FLOW_URI:
measurement_intent.set_measurement_type(ip_constants.MEASUREMENT_TYPE_FLOW)
elif opil_measurement_type.type == ip_constants.NCIT_RNA_SEQ_URI:
measurement_intent.set_measurement_type(ip_constants.MEASUREMENT_TYPE_RNA_SEQ)
elif opil_measurement_type.type == ip_constants.NCIT_DNA_SEQ_URI:
measurement_intent.set_measurement_type(ip_constants.MEASUREMENT_TYPE_DNA_SEQ)
elif opil_measurement_type.type == ip_constants.NCIT_PROTEOMICS_URI:
measurement_intent.set_measurement_type(ip_constants.MEASUREMENT_TYPE_PROTEOMICS)
elif opil_measurement_type.type == ip_constants.NCIT_SEQUENCING_CHROMATOGRAM_URI:
measurement_intent.set_measurement_type(ip_constants.MEASUREMENT_TYPE_SEQUENCING_CHROMATOGRAM)
elif opil_measurement_type.type == ip_constants.SD2_AUTOMATED_TEST_URI:
measurement_intent.set_measurement_type(ip_constants.MEASUREMENT_TYPE_AUTOMATED_TEST)
elif opil_measurement_type.type == ip_constants.NCIT_CFU_URI:
measurement_intent.set_measurement_type(ip_constants.MEASUREMENT_TYPE_CFU)
elif opil_measurement_type.type == ip_constants.NCIT_PLATE_READER_URI:
measurement_intent.set_measurement_type(ip_constants.MEASUREMENT_TYPE_PLATE_READER)
elif opil_measurement_type.type == ip_constants.SD2_CONDITION_SPACE_URI:
measurement_intent.set_measurement_type(ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE)
elif opil_measurement_type.type == ip_constants.SD2_EXPERIMENTAL_DESIGN_URI:
measurement_intent.set_measurement_type(ip_constants.MEASUREMENT_TYPE_EXPERIMENTAL_DESIGN)
elif opil_measurement_type.type == ip_constants.NCIT_FLUORESCENCE_MICROSCOPY:
measurement_intent.set_measurement_type(ip_constants.MEASUREMENT_TYPE_FLUOESCENE_MICROSCOPY)
else:
message = 'Measurement-type %s not supported in Intent parser' % opil_measurement_type.type
self.validation_errors.append(message)
continue
self._measurement_intents.append(measurement_intent)
def _process_row(self, row_index, control_data):
row = self._intent_parser_table.get_row(row_index)
measurement = MeasurementIntent()
content_intent = ContentIntent()
row_offset = row_index # Used for reporting row value to users
for cell_index in range(len(row)):
cell = self._intent_parser_table.get_cell(row_index, cell_index)
# Cell type based on column header
header_cell = self._intent_parser_table.get_cell(
self._intent_parser_table.header_row_index(), cell_index)
cell_type = cell_parser.PARSER.get_header_type(
header_cell.get_text())
column_offset = cell_index # Used for reporting column value to users
if not cell.get_text().strip() or cell_type in self.IGNORE_COLUMNS:
continue
if ip_constants.HEADER_MEASUREMENT_TYPE_TYPE == cell_type:
self._process_measurement_type(cell, measurement, row_offset,
column_offset)
elif ip_constants.HEADER_FILE_TYPE_TYPE == cell_type:
self._process_file_type(cell, measurement, row_offset,
column_offset)
elif ip_constants.HEADER_REPLICATE_TYPE == cell_type:
self._process_replicate(cell, measurement, row_offset,
column_offset)
elif ip_constants.HEADER_STRAINS_TYPE == cell_type:
self._process_strains(cell, measurement, row_offset,
column_offset)
elif ip_constants.HEADER_ODS_TYPE == cell_type:
self._process_ods(cell, measurement, row_offset, column_offset)
elif ip_constants.HEADER_TEMPERATURE_TYPE == cell_type:
self._process_temperature(cell, measurement, row_offset,
column_offset)
elif ip_constants.HEADER_TIMEPOINT_TYPE == cell_type:
self._process_timepoints(cell, measurement, row_offset,
column_offset)
elif ip_constants.HEADER_BATCH_TYPE == cell_type:
self._process_batch(cell, measurement, row_offset,
column_offset)
elif ip_constants.HEADER_CONTROL_TYPE == cell_type:
self._process_control(cell, control_data, measurement)
elif ip_constants.HEADER_NUM_NEG_CONTROL_TYPE == cell_type:
num_neg_controls = self._process_num_neg_controls(
cell, row_offset, column_offset)
if num_neg_controls:
content_intent.set_numbers_of_negative_controls(
num_neg_controls)
elif ip_constants.HEADER_RNA_INHIBITOR_REACTION_TYPE == cell_type:
rna_inhibitor_reactions = self._process_rna_inhibitor_reaction(
cell, row_offset, column_offset)
if rna_inhibitor_reactions:
content_intent.set_rna_inhibitor_reaction_flags(
rna_inhibitor_reactions)
elif ip_constants.HEADER_DNA_REACTION_CONCENTRATION_TYPE == cell_type:
dna_reaction_concentrations = self._process_dna_reaction_concentration(
cell, row_offset, column_offset)
if dna_reaction_concentrations:
content_intent.set_dna_reaction_concentrations(
dna_reaction_concentrations)
elif ip_constants.HEADER_TEMPLATE_DNA_TYPE == cell_type:
dna_templates = self._process_template_dna(
cell, row_offset, column_offset)
if dna_templates:
content_intent.set_template_dna_values(dna_templates)
elif ip_constants.HEADER_COLUMN_ID_TYPE == cell_type:
column_ids = self._process_col_id(cell, row_offset,
column_offset)
if column_ids:
content_intent.set_column_ids(column_ids)
elif ip_constants.HEADER_ROW_ID_TYPE == cell_type:
row_ids = self._process_row_id(cell, row_offset, column_offset)
if row_ids:
content_intent.set_row_ids(row_ids)
elif ip_constants.HEADER_MEASUREMENT_LAB_ID_TYPE == cell_type:
lab_ids = self._process_lab_id(cell, row_offset, column_offset)
if lab_ids:
content_intent.set_lab_ids(lab_ids)
else:
reagents_and_medias = self._process_reagent_or_media(
cell, header_cell, row_offset, column_offset)
self._processed_reagents_and_medias.extend(reagents_and_medias)
self._has_medias_and_reagents = True
for reagent_or_media in reagents_and_medias:
if isinstance(reagent_or_media, ReagentIntent):
content_intent.add_reagent(reagent_or_media)
elif isinstance(reagent_or_media, MediaIntent):
content_intent.add_media(reagent_or_media)
else:
self._validation_errors.append(
'Expected to process reagent or media but got %s' %
isinstance(reagent_or_media))
if not content_intent.is_empty():
measurement.add_content(content_intent)
return measurement
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()
def test_measurement_with_missing_file_type(self):
measurement_intent = MeasurementIntent()
measurement_intent.set_measurement_type(
ip_constants.MEASUREMENT_TYPE_CONDITION_SPACE)
with self.assertRaises(IntentParserException):
measurement_intent.to_structured_request()