def setUp(self) -> None:
config_file = os.path.join(self.resources_folder,
'submission_config.yml')
load_config(config_file)
# Need to set the directory so that the relative path set in the config file works from the top directory
os.chdir(ROOT_DIR)
self.validation = EloadValidation(2)
def main():
argparse = ArgumentParser(description='Prepare to process backlog study and validate VCFs.')
argparse.add_argument('--eload', required=True, type=int, help='The ELOAD number for this submission')
argparse.add_argument('--force_config', action='store_true', default=False,
help='Overwrite the configuration file after backing it up.')
argparse.add_argument('--debug', action='store_true', default=False,
help='Set the script to output logging information at debug level')
args = argparse.parse_args()
log_cfg.add_stdout_handler()
if args.debug:
log_cfg.set_log_level(logging.DEBUG)
# Load the config_file from default location
load_config()
preparation = EloadBacklog(args.eload)
preparation.fill_in_config(args.force_config)
preparation.report()
validation = EloadValidation(args.eload)
validation_tasks = ['assembly_check', 'vcf_check']
validation.validate(validation_tasks)
logger.info('Preparation complete, if files are valid please run ingestion as normal.')
def setUp(self) -> None:
config_file = os.path.join(self.resources_folder, 'submission_config.yml')
load_config(config_file)
# Need to set the directory so that the relative path set in the config file works from the top directory
os.chdir(ROOT_DIR)
self.validation = EloadValidation(2)
# Used to restore test config after each test
self.original_cfg = deepcopy(self.validation.eload_cfg.content)
def main():
argparse = ArgumentParser(description='Validate an ELOAD by checking the data and metadata format and semantics.')
argparse.add_argument('--eload', required=True, type=int, help='The ELOAD number for this submission')
argparse.add_argument('--validation_tasks', required=False, type=str, nargs='+',
default=EloadValidation.all_validation_tasks, choices=EloadValidation.all_validation_tasks,
help='task or set of tasks to perform during validation')
argparse.add_argument('--set_as_valid', action='store_true', default=False,
help='Set the script to consider all validation tasks performed as valid in the final '
'evaluation. This does not affect the actual report but only change the final '
'evaluation')
argparse.add_argument('--merge_per_analysis', action='store_true', default=False,
help='Whether to merge vcf files per analysis if possible.')
argparse.add_argument('--report', action='store_true', default=False,
help='Set the script to only report the results based on previously run validation.')
argparse.add_argument('--debug', action='store_true', default=False,
help='Set the script to output logging information at debug level')
args = argparse.parse_args()
log_cfg.add_stdout_handler()
if args.debug:
log_cfg.set_log_level(logging.DEBUG)
# Load the config_file from default location
load_config()
eload = EloadValidation(args.eload)
eload.upgrade_config_if_needed()
if not args.report:
eload.validate(args.validation_tasks, args.set_as_valid, args.merge_per_analysis)
eload.report()
class TestEloadValidation(TestCase):
resources_folder = os.path.join(ROOT_DIR, 'tests', 'resources')
def setUp(self) -> None:
config_file = os.path.join(self.resources_folder,
'submission_config.yml')
load_config(config_file)
# Need to set the directory so that the relative path set in the config file works from the top directory
os.chdir(ROOT_DIR)
self.validation = EloadValidation(2)
def test_parse_assembly_check_log_failed(self):
assembly_check_log = os.path.join(self.resources_folder, 'validations',
'failed_assembly_check.log')
expected = ([
" The assembly checking could not be completed: Contig '8' not found in assembly report"
], 1, 0, 0)
assert self.validation.parse_assembly_check_log(
assembly_check_log) == expected
def test_parse_assembly_check_report_mismatch(self):
mismatch_assembly_report = os.path.join(
self.resources_folder, 'validations',
'mismatch_text_assembly_report.txt')
expected = ([
"Line 15: Chromosome Chr14, position 7387, reference allele 'T' does not match the reference sequence, expected 'C'",
"Line 18: Chromosome Chr14, position 8795, reference allele 'A' does not match the reference sequence, expected 'G'",
"Line 19: Chromosome Chr14, position 8796, reference allele 'C' does not match the reference sequence, expected 'T'",
"Line 20: Chromosome Chr14, position 9033, reference allele 'G' does not match the reference sequence, expected 'A'",
"Line 22: Chromosome Chr14, position 9539, reference allele 'C' does not match the reference sequence, expected 'T'",
"Line 24: Chromosome Chr14, position 9558, reference allele 'C' does not match the reference sequence, expected 'T'",
"Line 38: Chromosome Chr14, position 10200, reference allele 'A' does not match the reference sequence, expected 'c'",
"Line 49: Chromosome Chr14, position 10875, reference allele 'G' does not match the reference sequence, expected 'C'",
"Line 54: Chromosome Chr14, position 11665, reference allele 'A' does not match the reference sequence, expected 'T'",
"Line 55: Chromosome Chr14, position 11839, reference allele 'G' does not match the reference sequence, expected 'a'"
], 14)
assert self.validation.parse_assembly_check_report(
mismatch_assembly_report) == expected
def test_parse_vcf_check_report(self):
vcf_check_report = os.path.join(self.resources_folder, 'validations',
'failed_file.vcf.errors.txt')
valid, error_list, nb_error, nb_warning = self.validation.parse_vcf_check_report(
vcf_check_report)
assert valid is False
assert len(error_list) == 8
assert nb_error == 8
assert nb_warning == 1
def test_report(self):
expected_report = '''Validation performed on 2020-11-01 10:37:54.755607
Metadata check: PASS
VCF check: PASS
Assembly check: PASS
Sample names check: PASS
----------------------------------
Metadata check:
* /path/to/spreadsheet: PASS
- number of error: 0
- error messages:
----------------------------------
VCF check:
* test.vcf: PASS
- number of error: 0
- number of warning: 2
- first 10 errors:
- see report for detail: /path/to/report
----------------------------------
Assembly check:
* test.vcf: PASS
- number of error: 0
- match results: 20/20 (100.0%)
- first 10 errors:
- first 10 mismatches:
- see report for detail: /path/to/report
----------------------------------
Sample names check:
* a1: PASS
- Samples that appear in the VCF but not in the Metadata sheet:
- Samples that appear in the Metadata sheet but not in the VCF file(s):
----------------------------------
'''
with patch('builtins.print') as mprint:
self.validation.report()
mprint.assert_called_once_with(expected_report)
class TestEloadValidation(TestCase):
resources_folder = os.path.join(ROOT_DIR, 'tests', 'resources')
def setUp(self) -> None:
config_file = os.path.join(self.resources_folder, 'submission_config.yml')
load_config(config_file)
# Need to set the directory so that the relative path set in the config file works from the top directory
os.chdir(ROOT_DIR)
self.validation = EloadValidation(2)
# Used to restore test config after each test
self.original_cfg = deepcopy(self.validation.eload_cfg.content)
def tearDown(self):
self.validation.eload_cfg.content = self.original_cfg
def test_parse_assembly_check_log_failed(self):
assembly_check_log = os.path.join(self.resources_folder, 'validations', 'failed_assembly_check.log')
expected = (
[" The assembly checking could not be completed: Contig '8' not found in assembly report"],
1,
0,
0
)
assert self.validation.parse_assembly_check_log(assembly_check_log) == expected
def test_parse_assembly_check_report_mismatch(self):
mismatch_assembly_report = os.path.join(self.resources_folder, 'validations', 'mismatch_text_assembly_report.txt')
expected = (
[
"Line 15: Chromosome Chr14, position 7387, reference allele 'T' does not match the reference sequence, expected 'C'",
"Line 18: Chromosome Chr14, position 8795, reference allele 'A' does not match the reference sequence, expected 'G'",
"Line 19: Chromosome Chr14, position 8796, reference allele 'C' does not match the reference sequence, expected 'T'",
"Line 20: Chromosome Chr14, position 9033, reference allele 'G' does not match the reference sequence, expected 'A'",
"Line 22: Chromosome Chr14, position 9539, reference allele 'C' does not match the reference sequence, expected 'T'",
"Line 24: Chromosome Chr14, position 9558, reference allele 'C' does not match the reference sequence, expected 'T'",
"Line 38: Chromosome Chr14, position 10200, reference allele 'A' does not match the reference sequence, expected 'c'",
"Line 49: Chromosome Chr14, position 10875, reference allele 'G' does not match the reference sequence, expected 'C'",
"Line 54: Chromosome Chr14, position 11665, reference allele 'A' does not match the reference sequence, expected 'T'",
"Line 55: Chromosome Chr14, position 11839, reference allele 'G' does not match the reference sequence, expected 'a'"
],
14, [], 0
)
assert self.validation.parse_assembly_check_report(mismatch_assembly_report) == expected
def test_parse_assembly_check_report_duplicate_synonym(self):
mismatch_assembly_report = os.path.join(self.resources_folder, 'validations', 'multiple_synonyms_text_assembly_report.txt')
expected = (
[], 0,
[
"Line 3: Multiple synonyms found for contig '1' in FASTA index file: CM000663.1 NC_000001.10",
"Line 4: Multiple synonyms found for contig 'X' in FASTA index file: CM000685.1 NC_000023.10"
],
2
)
assert self.validation.parse_assembly_check_report(mismatch_assembly_report) == expected
def test_parse_vcf_check_report(self):
vcf_check_report = os.path.join(self.resources_folder, 'validations', 'failed_file.vcf.errors.txt')
valid, error_list, nb_error, nb_warning = self.validation.parse_vcf_check_report(vcf_check_report)
assert valid is False
assert len(error_list) == 8
assert nb_error == 8
assert nb_warning == 1
def test_report(self):
expected_report = '''Validation performed on 2020-11-01 10:37:54.755607
Metadata check: PASS
VCF check: PASS
Assembly check: PASS
Sample names check: PASS
Aggregation check: PASS
----------------------------------
Metadata check:
* /path/to/spreadsheet: PASS
- number of error: 0
- error messages:
----------------------------------
VCF check:
* test.vcf: PASS
- number of error: 0
- number of warning: 2
- first 10 errors:
- see report for detail: /path/to/report
----------------------------------
Assembly check:
* test.vcf: PASS
- number of error: 0
- match results: 20/20 (100.0%)
- first 10 errors:
- first 10 mismatches:
- see report for detail: /path/to/report
----------------------------------
Sample names check:
* a1: PASS
- Samples that appear in the VCF but not in the Metadata sheet:
- Samples that appear in the Metadata sheet but not in the VCF file(s):
----------------------------------
Aggregation:
* a1: none
* Errors:
----------------------------------
VCF merge:
Merge types:
* a1: horizontal
----------------------------------
'''
with patch('builtins.print') as mprint:
self.validation.report()
mprint.assert_called_once_with(expected_report)
def test_detect_and_optionally_merge(self):
original_content = deepcopy(self.validation.eload_cfg.content)
analysis_alias = 'alias'
valid_files = ['file1', 'file2']
merged_files = {analysis_alias: 'merged.vcf.gz'}
self.validation.eload_cfg.set('validation', 'valid', 'analyses', analysis_alias, 'vcf_files', value=valid_files)
with patch('eva_submission.eload_validation.detect_merge_type', return_value=MergeType.HORIZONTAL), \
patch.object(VCFMerger, 'horizontal_merge', return_value=merged_files):
# Should detect merge type but not actually merge
self.validation.detect_and_optionally_merge(False)
self.assertEqual(
self.validation.eload_cfg.query('validation', 'merge_type', analysis_alias),
MergeType.HORIZONTAL.value
)
self.assertEqual(
self.validation.eload_cfg.query('validation', 'valid', 'analyses', analysis_alias, 'vcf_files'),
valid_files
)
# Should perform the merge
self.validation.detect_and_optionally_merge(True)
self.assertEqual(
self.validation.eload_cfg.query('validation', 'valid', 'analyses', analysis_alias, 'vcf_files'),
['merged.vcf.gz']
)
self.validation.eload_cfg.content = original_content
def test_merge_multiple_analyses(self):
valid_files = {
'horizontal': ['h1', 'h2'],
'vertical': ['v1', 'v2'],
'neither': ['n1', 'n2']
}
detections = [MergeType.HORIZONTAL, MergeType.VERTICAL, None]
horiz_merged_files = {'horizontal': 'h.vcf.gz'}
vert_merged_files = {'vertical': 'v.vcf.gz'}
for analysis_alias, vcf_files in valid_files.items():
self.validation.eload_cfg.set('validation', 'valid', 'analyses',
analysis_alias, 'vcf_files', value=vcf_files)
with patch('eva_submission.eload_validation.detect_merge_type', side_effect=detections), \
patch.object(VCFMerger, 'horizontal_merge', return_value=horiz_merged_files), \
patch.object(VCFMerger, 'vertical_merge', return_value=vert_merged_files):
self.validation.detect_and_optionally_merge(True)
self.assertEqual(
self.validation.eload_cfg.query('validation', 'valid', 'analyses', 'horizontal', 'vcf_files'),
['h.vcf.gz']
)
self.assertEqual(
self.validation.eload_cfg.query('validation', 'valid', 'analyses', 'vertical', 'vcf_files'),
['v.vcf.gz']
)
self.assertEqual(
self.validation.eload_cfg.query('validation', 'valid', 'analyses', 'neither', 'vcf_files'),
['n1', 'n2']
)
def test_merge_multiple_analyses_same_name(self):
valid_files = {
'a!': ['h1', 'h2'],
'a@': ['v1', 'v2'],
'a2': ['n1', 'n2']
}
detections = [MergeType.HORIZONTAL, MergeType.VERTICAL, None]
analyses_dict = {
analysis_alias: {'vcf_files': vcf_files}
for analysis_alias, vcf_files in valid_files.items()
}
self.validation.eload_cfg.set('validation', 'valid', 'analyses', value=analyses_dict)
with patch('eva_submission.eload_validation.detect_merge_type', side_effect=detections):
self.validation.detect_and_optionally_merge(True)
# Valid files should be unchanged even though merge is detected
self.assertEqual(self.validation.eload_cfg.query('validation', 'valid', 'analyses'), analyses_dict)
self.assertEqual(
self.validation.eload_cfg.query('validation', 'merge_errors'),
['Analysis aliases not valid as unique merged filenames']
)
def main():
validation_tasks = ['aggregation_check', 'assembly_check', 'vcf_check']
forced_validation_tasks = ['metadata_check', 'sample_check']
argparse = ArgumentParser(
description='Prepare to process backlog study and validate VCFs.')
argparse.add_argument('--eload',
required=True,
type=int,
help='The ELOAD number for this submission')
argparse.add_argument(
'--project_accession',
required=False,
type=str,
help='Set this project instead of the one associated with this eload. '
'Useful when the association is not set in the database. '
'The project needs to exists in the DB.')
argparse.add_argument(
'--analysis_accessions',
required=False,
type=str,
nargs='+',
help=
'Set these analysis instead of the ones associated with the project. '
'Useful when wanting to use a subset of the analysis. '
'The analyses need to exists in the DB.')
argparse.add_argument(
'--force_config',
action='store_true',
default=False,
help='Overwrite the configuration file after backing it up.')
argparse.add_argument(
'--keep_config',
action='store_true',
default=False,
help=
'Keep the configuration file as it is and only run the validation on it.'
)
argparse.add_argument(
'--validation_tasks',
required=False,
type=str,
nargs='+',
default=validation_tasks,
choices=validation_tasks,
help='task or set of tasks to perform during validation')
argparse.add_argument(
'--merge_per_analysis',
action='store_true',
default=False,
help='Whether to merge vcf files per analysis if possible.')
argparse.add_argument(
'--set_as_valid',
action='store_true',
default=False,
help=
'Set the script to consider all validation tasks performed as valid in the final '
'evaluation. This does not affect the actual report but only change the final '
'evaluation')
argparse.add_argument(
'--report',
action='store_true',
default=False,
help=
'Set the script to only report the results based on previously run preparation.'
)
argparse.add_argument(
'--debug',
action='store_true',
default=False,
help='Set the script to output logging information at debug level')
args = argparse.parse_args()
log_cfg.add_stdout_handler()
if args.debug:
log_cfg.set_log_level(logging.DEBUG)
# Load the config_file from default location
load_config()
with EloadBacklog(
args.eload,
project_accession=args.project_accession,
analysis_accessions=args.analysis_accessions) as preparation:
# Pass the eload config object to validation so that the two objects share the same state
with EloadValidation(args.eload, preparation.eload_cfg) as validation:
if not args.report and not args.keep_config:
preparation.fill_in_config(args.force_config)
if not args.report:
validation.validate(args.validation_tasks)
# Also mark the other validation tasks as force so they are all passable
if args.set_as_valid:
forced_validation_tasks = validation.all_validation_tasks
for validation_task in forced_validation_tasks:
validation.eload_cfg.set('validation',
validation_task,
'forced',
value=True)
validation.mark_valid_files_and_metadata(
args.merge_per_analysis)
if args.merge_per_analysis:
preparation.copy_valid_config_to_brokering_after_merge()
preparation.report()
validation.report()
logger.info(
'Preparation complete, if files are valid please run ingestion as normal.'
)