def test_expansion(self):
"""Test basic expansion of combinatorial derivations"""
doc = sbol3.Document()
doc.read(os.path.join(TESTFILE_DIR, 'simple_library.nt'))
sbol3.set_namespace('http://sbolstandard.org/testfiles')
roots = list(
sbol_utilities.expand_combinatorial_derivations.
root_combinatorial_derivations(doc))
assert len(
roots) == 1, f'Unexpected roots: {[r.identity for r in roots]}'
derivative_collections = sbol_utilities.expand_combinatorial_derivations.expand_derivations(
roots)
assert not len(doc.validate())
assert len(doc.find('Round_1_order_collection').members) == 24
output_doc = sbol3.Document()
for c in derivative_collections:
copy_toplevel_and_dependencies(output_doc, c)
assert not len(output_doc.validate())
temp_name = tempfile.mkstemp(suffix='.nt')[1]
output_doc.write(temp_name, sbol3.SORTED_NTRIPLES)
assert_files_identical(
temp_name, os.path.join(TESTFILE_DIR,
'expanded_simple_library.nt'))
def test_custom_conversion(self):
"""Test if conversion works correctly when the config us used to change expected sheet structure"""
wb = openpyxl.load_workbook(os.path.join(
TESTFILE_DIR, 'nonstandard_simple_library.xlsx'),
data_only=True)
sbol3.set_namespace('http://sbolstandard.org/testfiles')
config = {
'basic_parts_name': 'C2',
'basic_parts_description': 'A12',
'basic_first_row': 21,
'basic_role_col': 2,
'basic_notes_col': 3,
'basic_description_col': 5,
'basic_source_prefix_col': 6,
'basic_source_id_col': 7,
'basic_final_col': 10,
'basic_circular_col': 11,
'basic_length_col': 12,
'basic_sequence_col': 13,
'composite_first_part_col': 8
}
doc = sbol_utilities.excel_to_sbol.excel_to_sbol(wb, config)
assert not doc.validate().errors and not doc.validate().warnings
assert len(doc.find('BasicParts').members) == 26
assert len(doc.find('CompositeParts').members) == 6
assert len(doc.find('LinearDNAProducts').members) == 2
assert len(doc.find('FinalProducts').members) == 2
temp_name = tempfile.mkstemp(suffix='.nt')[1]
doc.write(temp_name, sbol3.SORTED_NTRIPLES)
assert_files_identical(temp_name,
os.path.join(TESTFILE_DIR, 'simple_library.nt'))
def test_commandline(self):
"""Test expansion of combinatorial derivations from command line"""
temp_name = tempfile.mkstemp(suffix='.nt')[1]
test_args = [
'sbol-expand-derivations', '-vv',
os.path.join(TESTFILE_DIR, 'simple_library.nt'), '-o', temp_name
]
with patch.object(sys, 'argv', test_args):
sbol_utilities.expand_combinatorial_derivations.main()
assert_files_identical(
temp_name, os.path.join(TESTFILE_DIR,
'expanded_simple_library.nt'))
def test_commandline(self):
"""Make sure function works correctly when run from the command line"""
temp_name = tempfile.mkstemp(suffix='.nt')[1]
test_args = [
'excel-to-sbol', '-vv',
os.path.join(TESTFILE_DIR, 'simple_library.xlsx'), '-o', temp_name,
'-n', 'http://sbolstandard.org/testfiles'
]
with patch.object(sys, 'argv', test_args):
sbol_utilities.excel_to_sbol.main()
assert_files_identical(temp_name,
os.path.join(TESTFILE_DIR, 'simple_library.nt'))
def test_multi_backbone(self):
"""Check if generation works correclty when there is more than one backbone option"""
wb = openpyxl.load_workbook(os.path.join(TESTFILE_DIR,
'two_backbones.xlsx'),
data_only=True)
sbol3.set_namespace('http://sbolstandard.org/testfiles')
doc = sbol_utilities.excel_to_sbol.excel_to_sbol(wb)
assert not doc.validate().errors and not doc.validate().warnings
assert len(doc.find('BasicParts').members) == 9
assert len(doc.find('CompositeParts').members) == 2
assert len(doc.find('LinearDNAProducts').members) == 2
assert len(doc.find('FinalProducts').members) == 2
temp_name = tempfile.mkstemp(suffix='.nt')[1]
doc.write(temp_name, sbol3.SORTED_NTRIPLES)
assert_files_identical(temp_name,
os.path.join(TESTFILE_DIR, 'two_backbones.nt'))
def test_constraints(self):
"""Check if constraints are generated correctly"""
wb = openpyxl.load_workbook(os.path.join(TESTFILE_DIR,
'constraints_library.xlsx'),
data_only=True)
sbol3.set_namespace('http://sbolstandard.org/testfiles')
doc = sbol_utilities.excel_to_sbol.excel_to_sbol(wb)
assert not doc.validate().errors and not doc.validate().warnings
assert len(doc.find('BasicParts').members) == 43
assert len(doc.find('CompositeParts').members) == 8
assert len(doc.find('LinearDNAProducts').members) == 2
assert len(doc.find('FinalProducts').members) == 2
temp_name = tempfile.mkstemp(suffix='.nt')[1]
doc.write(temp_name, sbol3.SORTED_NTRIPLES)
assert_files_identical(
temp_name, os.path.join(TESTFILE_DIR, 'constraints_library.nt'))
def test_conversion(self):
"""Basic smoke test of Excel to SBOL3 conversion"""
wb = openpyxl.load_workbook(os.path.join(TESTFILE_DIR,
'simple_library.xlsx'),
data_only=True)
sbol3.set_namespace('http://sbolstandard.org/testfiles')
doc = sbol_utilities.excel_to_sbol.excel_to_sbol(wb)
assert not doc.validate().errors and not doc.validate().warnings
assert len(doc.find('BasicParts').members) == 26
assert len(doc.find('CompositeParts').members) == 6
assert len(doc.find('LinearDNAProducts').members) == 2
assert len(doc.find('FinalProducts').members) == 2
temp_name = tempfile.mkstemp(suffix='.nt')[1]
doc.write(temp_name, sbol3.SORTED_NTRIPLES)
assert_files_identical(temp_name,
os.path.join(TESTFILE_DIR, 'simple_library.nt'))