def test_wrongfiletype_validate_single_file():
"""
Tests that if there is no filetype for the filename passed
in, an error is thrown
"""
entitylist = [WRONG_NAME_ENT]
expected_error = ('----------------ERRORS----------------\n'
'Your filename is incorrect! Please change your '
'filename before you run the validator or specify '
'--filetype if you are running the validator locally')
with patch.object(validate.GenieValidationHelper,
"determine_filetype",
return_value=None) as mock_determine_filetype:
validator = validate.GenieValidationHelper(
syn=syn,
project_id=None,
center=CENTER,
entitylist=entitylist,
format_registry={'wrong': Mock()})
valid, message = validator.validate_single_file()
assert message == expected_error
assert not valid
mock_determine_filetype.assert_called_once_with()
def test_perfect_determine_filetype(filename_fileformat_map):
'''
Tests determining of file type through filenames
Parameters are passed in from filename_fileformat_map
'''
(filepath_list, fileformat) = filename_fileformat_map
validator = validate.GenieValidationHelper(syn, center, filepath_list)
assert validator.determine_filetype() == fileformat
def test_wrongfilename_noerror_determine_filetype():
'''
Tests None is passed back when wrong filename is passed
when raise_error flag is False
'''
filepathlist = ['wrong.txt']
validator = validate.GenieValidationHelper(syn,
center=center,
filepathlist=filepathlist)
assert validator.file_type is None
def test_filetype_validate_single_file():
'''
Tests that if filetype is passed in that an error is thrown
if it is an incorrect filetype
'''
filepathlist = ['clinical.txt']
center = "SAGE"
expected_error = "----------------ERRORS----------------\nYour filename is incorrect! Please change your filename before you run the validator or specify --filetype if you are running the validator locally"
validator = validate.GenieValidationHelper(syn, center, filepathlist)
valid, message, filetype = validator.validate_single_file()
assert message == expected_error
def test_perfect_determine_filetype():
"""
Tests determining of file type through filenames
Parameters are passed in from filename_fileformat_map
"""
filetype = "clincial"
ent_list = [SAMPLE_ENT]
with patch.object(FileFormat, "validateFilename", return_value=filetype):
validator = validate.GenieValidationHelper(
syn,
None,
CENTER,
ent_list,
format_registry={filetype: FileFormat})
assert validator.determine_filetype() == filetype
def test_wrongfilename_noerror_determine_filetype():
'''
Tests None is passed back when wrong filename is passed
when raise_error flag is False
'''
ent_list = [WRONG_NAME_ENT]
with patch.object(FileFormat,
"validateFilename",
side_effect=AssertionError):
validator = validate.GenieValidationHelper(
syn,
project_id=None,
center=CENTER,
entitylist=ent_list,
format_registry={"wrong": FileFormat})
assert validator.file_type is None
def test_wrongfiletype_validate_single_file():
'''
Tests that if there is no filetype for the filename passed
in, an error is thrown
'''
filepathlist = ['clinical.txt']
center = "SAGE"
expected_error = '----------------ERRORS----------------\nYour filename is incorrect! Please change your filename before you run the validator or specify --filetype if you are running the validator locally'
with mock.patch("genie.validate.GenieValidationHelper.determine_filetype",
return_value=None) as mock_determine_filetype:
validator = validate.GenieValidationHelper(syn=syn,
center=center,
filepathlist=filepathlist)
valid, message, filetype = validator.validate_single_file()
assert message == expected_error
mock_determine_filetype.assert_called_once_with()
def test_valid_validate_single_file():
"""
Tests that all the functions are run in validate single
file workflow and all the right things are returned
"""
entitylist = [CLIN_ENT]
error_string = ''
warning_string = ''
expected_valid = True
expected_message = "valid message here!"
expected_filetype = "clinical"
project_ent = Mock(id='syn1234')
with patch.object(syn, "get", return_value=project_ent),\
patch.object(validate.GenieValidationHelper,
"determine_filetype",
return_value=expected_filetype) as mock_determine_ftype,\
patch.object(FileFormat, "validate",
return_value=(expected_valid, error_string,
warning_string)) as mock_genie_class,\
patch.object(validate, "collect_errors_and_warnings",
return_value=expected_message) as mock_determine:
validator = validate.GenieValidationHelper(
syn,
project_id="syn1234",
center=CENTER,
entitylist=entitylist,
format_registry={'clinical': FileFormat})
valid, message = validator.validate_single_file(oncotree_link=None,
nosymbol_check=False)
assert valid == expected_valid
assert message == expected_message
assert validator.file_type == expected_filetype
mock_determine_ftype.assert_called_once_with()
mock_genie_class.assert_called_once_with(filePathList=[CLIN_ENT.path],
oncotree_link=None,
nosymbol_check=False,
project_id='syn1234')
mock_determine.assert_called_once_with(error_string, warning_string)
def test_valid_validate_single_file():
'''
Tests that all the functions are run in validate single
file workflow and all the right things are returned
'''
filepathlist = ['clinical.txt']
error_string = ''
warning_string = ''
center = 'SAGE'
expected_valid = True
expected_message = "valid message here!"
expected_filetype = "clinical"
with mock.patch(
"genie.validate.GenieValidationHelper.determine_filetype",
return_value=expected_filetype) as mock_determine_filetype,\
mock.patch(
"genie.clinical.clinical.validate",
return_value=(expected_valid, error_string, warning_string)) as mock_genie_class,\
mock.patch(
"genie.validate.collect_errors_and_warnings",
return_value=expected_message) as mock_determine:
validator = validate.GenieValidationHelper(syn,
center=center,
filepathlist=filepathlist)
valid, message, filetype = validator.validate_single_file(
oncotree_link=None, nosymbol_check=False)
assert valid == expected_valid
assert message == expected_message
assert filetype == expected_filetype
mock_determine_filetype.assert_called_once_with()
mock_genie_class.assert_called_once_with(filePathList=filepathlist,
oncotree_link=None,
nosymbol_check=False)
mock_determine.assert_called_once_with(error_string, warning_string)
def test_filetype_validate_single_file():
"""
Tests that if filetype is passed in that an error is thrown
if it is an incorrect filetype
"""
entitylist = [WRONG_NAME_ENT]
expected_error = ("----------------ERRORS----------------\n"
"Your filename is incorrect! Please change your "
"filename before you run the validator or specify "
"--filetype if you are running the validator locally")
with patch.object(FileFormat,
"validateFilename",
side_effect=AssertionError):
validator = validate.GenieValidationHelper(
syn,
None,
CENTER,
entitylist,
format_registry={'wrong': FileFormat})
valid, message = validator.validate_single_file()
assert message == expected_error
assert not valid