def get_nr_samples_excel(orderform_path: str) -> int:
"""Parse a excel orderform file and return the number of sample rows"""
orderform_parser = ExcelOrderformParser()
workbook: Workbook = openpyxl.load_workbook(
filename=orderform_path, read_only=True, data_only=True
)
sheet_name: str = orderform_parser.get_sheet_name(workbook.sheetnames)
orderform_sheet: Worksheet = workbook[sheet_name]
nr_samples = 0
current_row = "unknown"
for row in orderform_sheet.rows:
if row[0].value == "</SAMPLE ENTRIES>":
# End of samples
break
elif row[0].value == "<SAMPLE ENTRIES>":
# Samples start here
current_row = "samples"
continue
if current_row == "samples":
values = []
for cell in row:
value = str(cell.value)
if value == "None":
value = ""
values.append(value)
# skip empty rows
if values[0]:
nr_samples += 1
return nr_samples
def test_parse_rml_orderform(rml_orderform: str,
nr_samples_rml_orderform: int):
"""Test to parse an excel orderform in xlsx format"""
# GIVEN a orderform in excel format
assert is_excel(Path(rml_orderform))
# GIVEN a orderform API
order_form_parser = ExcelOrderformParser()
# GIVEN the correct orderform name
order_name: str = Path(rml_orderform).stem
# WHEN parsing the RML orderform
order_form_parser.parse_orderform(excel_path=rml_orderform)
# THEN assert that the correct name was set
assert order_form_parser.order_name == order_name
# THEN assert that the number of samples was correct
assert len(order_form_parser.samples) == nr_samples_rml_orderform
def test_parse_mip_orderform(mip_orderform: str,
nr_samples_mip_orderform: int):
"""Test to parse a mip orderform in xlsx format"""
# GIVEN a orderform in excel format
assert is_excel(Path(mip_orderform))
# GIVEN a orderform API
order_form_parser = ExcelOrderformParser()
# GIVEN the correct orderform name
order_name: str = Path(mip_orderform).stem
# WHEN parsing the mip orderform
order_form_parser.parse_orderform(excel_path=mip_orderform)
# THEN assert the number of samples parsed are correct
assert len(order_form_parser.samples) == nr_samples_mip_orderform
# THEN assert that the project type is correct
assert order_form_parser.project_type == str(Pipeline.MIP_DNA)
def test_parse_metagenome_orderform(metagenome_orderform: str):
"""Test to parse an metagenome orderform in excel format"""
# GIVEN a order form in excel format
assert is_excel(Path(metagenome_orderform))
# GIVEN a orderform API
orderform_parser: ExcelOrderformParser = ExcelOrderformParser()
# WHEN parsing the orderform
orderform_parser.parse_orderform(excel_path=metagenome_orderform)
# THEN assert that the project type is correct
assert orderform_parser.project_type == OrderType.METAGENOME
def test_parse_microbial_orderform(microbial_orderform: str):
"""Test to parse a microbial orderform in excel format"""
# GIVEN a order form in excel format
assert is_excel(Path(microbial_orderform))
# GIVEN a orderform API
orderform_parser: ExcelOrderformParser = ExcelOrderformParser()
# WHEN parsing the orderform
orderform_parser.parse_orderform(excel_path=microbial_orderform)
# THEN assert that the project type is correct
assert orderform_parser.project_type == OrderType.MICROSALT
def test_parse_balsamic_orderform(balsamic_orderform: str):
"""Test to parse an balsamic orderform in excel format"""
# GIVEN a orderform in excel format
assert is_excel(Path(balsamic_orderform))
# GIVEN a orderform API
orderform_parser: ExcelOrderformParser = ExcelOrderformParser()
# WHEN parsing the orderform
orderform_parser.parse_orderform(excel_path=balsamic_orderform)
# THEN assert that the project type is correct
assert orderform_parser.project_type == OrderType.BALSAMIC
def test_generate_parsed_rml_orderform(rml_order_parser: ExcelOrderformParser,
caplog):
"""Test to generate a order from a parsed rml excel file"""
# GIVEN a order form parser that have parsed an excel file
# WHEN generating the order
order: Orderform = rml_order_parser.generate_orderform()
# THEN assert that some samples where parsed and found
assert order.samples
# THEN assert that no cases where found since this is an RML order
assert not order.cases
def test_parse_sarscov2_orderform(sarscov2_orderform: str):
"""Test to parse a sarscov2 orderform in excel format"""
# GIVEN a order form in excel format
assert is_excel(Path(sarscov2_orderform))
# GIVEN a orderform API
orderform_parser: ExcelOrderformParser = ExcelOrderformParser()
# WHEN parsing the orderform
orderform_parser.parse_orderform(excel_path=sarscov2_orderform)
# THEN assert that the project type is correct
assert orderform_parser.project_type == OrderType.SARS_COV_2
def test_parse_fastq_orderform(fastq_orderform: str,
nr_samples_fastq_orderform: int):
"""Test to parse an fastq orderform in xlsx format"""
# GIVEN a orderform in excel format
assert is_excel(Path(fastq_orderform))
# GIVEN a orderform API
order_form_parser = ExcelOrderformParser()
# GIVEN the correct orderform name
order_name: str = Path(fastq_orderform).stem
# WHEN parsing the fastq orderform
order_form_parser.parse_orderform(excel_path=fastq_orderform)
# THEN assert that the correct name was set
assert order_form_parser.order_name == order_name
# THEN assert that the correct number if samples where parsed
assert len(order_form_parser.samples) == nr_samples_fastq_orderform
# THEN it should determine the project type
assert order_form_parser.project_type == str(Pipeline.FASTQ)
# THEN it should determine the correct customer should have been parsed
assert order_form_parser.customer_id == "cust000"
def test_generate_mip_orderform_with_cases(
mip_order_parser: ExcelOrderformParser):
"""Test to parse a mip orderform with cases"""
# GIVEN a mip orderform parser
# WHEN generating a orderform
orderform: Orderform = mip_order_parser.generate_orderform()
# THEN assert that there where cases in the order
assert len(orderform.cases) > 0
case_obj = orderform.cases[0]
assert len(case_obj.samples) == 3
assert case_obj.name == "mipdnacase1"
assert case_obj.priority == "research"
assert set(case_obj.panels) == set(["AD-HSP", "Ataxi", "Actionable"])
def fixture_fastq_order_parser(fastq_orderform: str) -> ExcelOrderformParser:
"""Return a orderform parser that have parsed an orderform in excel format"""
order_form_parser = ExcelOrderformParser()
order_form_parser.parse_orderform(excel_path=fastq_orderform)
return order_form_parser