def test_conversion(self):
success, study_id, validate = mw2isa_convert(studyid="ST000367",
outputdir=self._tmp_dir,
dl_option="no",
validate_option=True)
# exit_code = sys.exit()
if success and validate:
log.info("conversion successful, invoking the validator for " +
study_id)
with open(
os.path.join(self._tmp_dir, study_id,
'i_investigation.txt')) as fp:
# print(isatab.dumps(isatab.load(fp)))
# fp.seek(0)
report = isatab.validate(fp)
print(report)
if len(report['errors']) > 0:
self.fail("conversion successful but validation failed")
else:
self.fail("conversion failed, validation was not invoked")
def test_info_reporting_bii_i_1_isatab(self):
test_case = 'BII-I-1'
with open(
os.path.join(utils.TAB_DATA_DIR, test_case,
'i_investigation.txt')) as test_case_fp:
report = isatab.validate(
fp=test_case_fp,
config_dir=utils.DEFAULT2015_XML_CONFIGS_DATA_DIR,
log_level=self._reporting_level)
self.assertIn(
{
'message': 'Found 18 study groups in s_BII-S-1.txt',
'supplemental': 'Found 18 study groups in s_BII-S-1.txt',
'code': 5001
}, report['info'])
self.assertIn(
{
'message': 'Found 9 study groups in a_proteome.txt',
'code': 5001,
'supplemental': 'Found 9 study groups in a_proteome.txt'
}, report['info'])
self.assertIn(
{
'message': 'Found 17 study groups in a_metabolome.txt',
'code': 5001,
'supplemental': 'Found 17 study groups in a_metabolome.txt'
}, report['info'])
self.assertIn(
{
'message': 'Found 12 study groups in a_transcriptome.txt',
'code': 5001,
'supplemental':
'Found 12 study groups in a_transcriptome.txt'
}, report['info'])
self.assertIn(
{
'message': 'Found 7 study groups in a_microarray.txt',
'code': 5001,
'supplemental': 'Found 7 study groups in a_microarray.txt'
}, report['info'])
def test_all_convert(self, client_mock1, client_mock2):
"""Test the full conversion from BrAPI to ISA using mock data and validating using ISA validator."""
# Mock API calls
instance_mock = client_mock1.return_value = client_mock2.return_value
instance_mock.get_trials.return_value = mock_data.mock_trials
instance_mock.get_study.return_value = mock_data.mock_study
instance_mock.get_study_germplasms.return_value = mock_data.mock_germplasms
instance_mock.get_study_observation_units.return_value = mock_data.mock_observation_units
instance_mock.get_study_observed_variables.return_value = mock_data.mock_variables
# Run full conversion
brapi_to_isa.main(None)
out_folder = brapi_to_isa.get_output_path(
mock_data.mock_trials[0]['trialName'])
assert os.path.exists(out_folder)
# TODO: use MIAPPE ISA configuration for validation here
investigation_file_path = os.path.join(out_folder,
'i_investigation.txt')
with open(investigation_file_path, 'r', encoding='utf-8') as i_fp:
assert isatab.validate(i_fp)
## Validation of ISA-Tab metadata produced manually and available in folder 'metadata-isa'
import os
import logging
from isatools import isatab
my_json_report = isatab.validate(open(
os.path.join('./metadata-isa/', 'i_gsk_longitudinal.txt')),
log_level=logging.WARN)
def test_get_experiment_as_isatab_mtab_20(self):
AX.get_isatab('E-MTAB-20',
self._tmp_dir) # gets E-MTAB-20 MAGE-TAB files
with open(os.path.join(self._tmp_dir, 'i_investigation.txt')) as i_fp:
isatab.validate(i_fp)
def test_get_experiment_as_isatab_mtab_1936(self): # splits three assays
AX.get_isatab('E-MTAB-1963',
self._tmp_dir) # gets E-MTAB-4649 MAGE-TAB files
with open(os.path.join(self._tmp_dir, 'i_investigation.txt')) as i_fp:
isatab.validate(i_fp)
def test_get_experiment_as_isatab_mtab_584(self):
AX.get_isatab('E-MTAB-584', self._tmp_dir)
with open(os.path.join(self._tmp_dir, 'i_investigation.txt')) as i_fp:
isatab.validate(i_fp)
def test_get_experiment_as_isatab_afmx_2(
self): # FIXME -> output ISA-Tab has many missing cells! WHY!?!?
AX.get_isatab('E-AFMX-2',
self._tmp_dir) # gets E-AFMX-2 MAGE-TAB files
with open(os.path.join(self._tmp_dir, 'i_investigation.txt')) as i_fp:
isatab.validate(i_fp)
with TemporaryDirectory() as tmpdirname:
print('Created temporary directory:', tmpdirname)
print('Converting files to UTF-8.')
for f in files:
with codecs.open(isa_tab_dir + os.sep + f, 'r') as file:
lines = file.read()
with codecs.open(tmpdirname + os.sep + f, 'w', encoding='utf8') as file:
file.write(lines)
# Validating ISA-TAB with configuration files
# -------------------------------------------
try:
print('Validating isa-tab files against configuration files found in ' + isa_config_dir)
validation_log_path = isa_tab_dir + os.sep + 'validation_log.json'
report = isatab.validate(
open(os.path.join(tmpdirname, 'i_investigation.txt')), isa_config_dir)
with open(validation_log_path, 'w') as out_fp2:
json.dump(report, out_fp2, indent=4)
print('VALIDATION FINISHED')
print("* Errors found: {}\n* Warnings found: {}\n* Info messages: {}".format(
len(report['errors']), len(report['warnings']), len(report['info'])))
print('The ISA-TAB validation log file can be found at: ' +
validation_log_path)
except Exception as ioe:
print('ISA-TAB validation failed!...')
print(str(ioe))
def test_exportISATAB(self):
nmrData = nPYc.NMRDataset('', fileType='empty')
raw_data = {
'Acquired Time': [
'2016-08-09 01:36:23', '2016-08-09 01:56:23',
'2016-08-09 02:16:23', '2016-08-09 02:36:23',
'2016-08-09 02:56:23'
],
'AssayRole': [
'AssayRole.LinearityReference', 'AssayRole.LinearityReference',
'AssayRole.LinearityReference', 'AssayRole.Assay',
'AssayRole.Assay'
],
#'SampleType': ['SampleType.StudyPool', 'SampleType.StudyPool', 'SampleType.StudyPool','SampleType.StudySample', 'SampleType.StudySample'],
'Status': [
'SampleType.StudyPool', 'SampleType.StudyPool',
'SampleType.StudyPool', 'SampleType.StudySample',
'SampleType.StudySample'
],
'Subject ID': ['', '', '', 'SCANS-120', 'SCANS-130'],
'Sampling ID': ['', '', '', 'T0-7-S', 'T0-9-S'],
'Sample File Name': ['sfn1', 'sfn2', 'sfn3', 'sfn4', 'sfn5'],
'Study':
['TestStudy', 'TestStudy', 'TestStudy', 'TestStudy', 'TestStudy'],
'Gender': ['', '', '', 'Female', 'Male'],
'Age': ['', '', '', '55', '66'],
'Sampling Date': ['', '', '', '27/02/2006', '28/02/2006'],
'Sample batch': ['', '', '', 'SB 1', 'SB 2'],
'Batch': ['1', '2', '3', '4', '5'],
'Run Order': ['0', '1', '2', '3', '4'],
'Instrument': ['QTOF 2', 'QTOF 2', 'QTOF 2', 'QTOF 2', 'QTOF 2'],
'Assay data name':
['', '', '', 'SS_LNEG_ToF02_S1W4', 'SS_LNEG_ToF02_S1W5']
}
nmrData.sampleMetadata = pandas.DataFrame(
raw_data,
columns=[
'Acquired Time', 'AssayRole', 'Status', 'Subject ID',
'Sampling ID', 'Study', 'Gender', 'Age', 'Sampling Date',
'Sample batch', 'Batch', 'Run Order', 'Instrument',
'Assay data name', 'Sample File Name'
])
with tempfile.TemporaryDirectory() as tmpdirname:
details = {
'investigation_identifier': "i1",
'investigation_title': "Give it a title",
'investigation_description': "Add a description",
'investigation_submission_date':
"2016-11-03", #use today if not specified
'investigation_public_release_date': "2016-11-03",
'first_name': "Noureddin",
'last_name': "Sadawi",
'affiliation': "University",
'study_filename': "my_nmr_study",
'study_material_type': "Serum",
'study_identifier': "s1",
'study_title': "Give the study a title",
'study_description': "Add study description",
'study_submission_date': "2016-11-03",
'study_public_release_date': "2016-11-03",
'assay_filename': "my_nmr_assay"
}
nmrData.initialiseMasks()
nmrData.exportDataset(destinationPath=tmpdirname,
isaDetailsDict=details,
saveFormat='ISATAB')
investigatio_file = os.path.join(tmpdirname, 'i_investigation.txt')
numerrors = 0
with open(investigatio_file) as fp:
report = isatab.validate(fp)
numerrors = len(report['errors'])
#self.assertTrue(os.path.exists(a))
self.assertEqual(
numerrors,
0,
msg="ISATAB Validator found {} errors in the ISA-Tab archive".
format(numerrors))
import os
from isatools import isatab
my_json_report = isatab.validate(
open(os.path.join('./metadata-isa/', 'i_gsk_longitudinal.txt')))
if os.path.isdir(input_path):
isatab_dir = input_path
else:
with zipfile.ZipFile(input_path) as zfp:
zfp.extractall(path=tmp_dir)
isatab_dir = tmp_dir
if not os.path.exists(tmp_dir):
print('File path to ISA files \'{}\' does not exist'.format(isatab_dir))
sys.exit(0)
report = None
i_files = glob.glob(os.path.join(isatab_dir, 'i_*.txt'))
if len(i_files) == 1:
i_file_name = next(iter(i_files))
with open(i_file_name) as in_fp:
json_report = isatab.validate(in_fp)
if json_report is not None:
with open(json_output_path, 'w') as out_fp:
json.dump(json_report, out_fp, indent=4)
import shutil
shutil.rmtree(tmp_dir)
def build_messages(messages):
messages_table = "No messages."
if len(messages) > 0:
messages_table = "<table>"
messages_table += "<tr><th>Code</th><th>Message</th><th>Supplemental information</th></tr>"
for message in messages:
messages_table += "<tr><td>{code}</td><td>{message}</td><td>{supplemental}</td></tr>".format(
code=message['code'],
