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 _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