def test_spot_descriptor_injection(self):
sra.export(self._inv_obj,
self._tmp_dir,
sra_settings=self._sra_default_config)
with open(os.path.join(self._tmp_dir, 'experiment_set.xml'),
'rb') as out_fp:
self.assertTrue('<SPOT_DESCRIPTOR>' in str(out_fp.read()))
def convert(json_fp,
path,
config_dir=None,
sra_settings=None,
datafilehashes=None,
validate_first=True):
""" Converter for ISA-JSON to SRA.
:param json_fp: File pointer to ISA JSON input
:param path: Directory for output SRA XMLs to be written
:param config_dir: path to JSON configuration. If none, uses default
embedded in API
:param sra_settings: SRA settings dict
:param datafilehashes: Data files with hashes, in a dict
"""
if validate_first:
log.info("Validating input JSON before conversion")
report = isajson.validate(fp=json_fp,
config_dir=config_dir,
log_level=logging.ERROR)
if len(report.get('errors')) > 0:
log.fatal("Could not proceed with conversion as there are some "
"validation errors. Check log.")
return
log.info("Loading isajson {}".format(json_fp.name))
isa = isajson.load(fp=json_fp)
log.info("Exporting SRA to {}".format(path))
log.debug("Using SRA settings ".format(sra_settings))
sra.export(isa,
path,
sra_settings=sra_settings,
datafilehashes=datafilehashes)
def test_sra_paired_export_run_set_xml(self):
sra.export(self._inv_obj,
self._tmp_dir,
sra_settings=self._sra_default_config)
with open(os.path.join(self._tmp_dir, 'run_set.xml'), 'rb') as out_fp:
actual_run_set_xml_obj = etree.fromstring(out_fp.read())
self.assertTrue(
utils.assert_xml_equal(self._expected_run_set_xml_obj,
actual_run_set_xml_obj))
def test_sra_export_sample_set_xml(self):
sra.export(self._inv_obj,
self._tmp_dir,
sra_settings=self._sra_default_config)
actual_sample_set_xml_obj = etree.fromstring(
open(os.path.join(self._tmp_dir, 'sample_set.xml'), 'rb').read())
self.assertTrue(
utils.assert_xml_equal(self._expected_sample_set_xml_obj,
actual_sample_set_xml_obj))
def convert(json_fp, path, config_dir=None, sra_settings=None, datafilehashes=None, validate_first=True):
""" (New) Converter for ISA JSON to SRA.
:param json_fp: File pointer to ISA JSON input
:param path: Directory for output to be written
:param config_dir: path to JSON configuration. If none, uses default embedded in API
:param sra_settings: SRA settings dict
:param datafilehashes: Data files with hashes, in a dict
"""
if validate_first:
log_msg_stream = isajson.validate(fp=json_fp, config_dir=config_dir, log_level=logging.WARNING)
if '(E)' in log_msg_stream.getvalue():
logger.fatal("Could not proceed with conversion as there are some validation errors. Check log.")
return
i = isajson.load(fp=json_fp)
sra.export(i, path, sra_settings=sra_settings, datafilehashes=datafilehashes)
def convert2(json_fp, path, config_dir=None, sra_settings=None, datafilehashes=None, validate_first=True):
""" (New) Converter for ISA JSON to SRA.
:param json_fp: File pointer to ISA JSON input
:param path: Directory for output to be written
:param config_dir: path to JSON configuration. If none, uses default embedded in API
:param sra_settings: SRA settings dict
:param datafilehashes: Data files with hashes, in a dict
"""
if validate_first:
log_msg_stream = isajson.validate(fp=json_fp, config_dir=config_dir, log_level=logging.WARNING)
if '(E)' in log_msg_stream.getvalue():
logger.fatal("Could not proceed with conversion as there are some validation errors. Check log.")
return
i = isajson.load(fp=json_fp)
sra.export(i, path, sra_settings=sra_settings, datafilehashes=datafilehashes)
def test_sra_export_project_set_xml(self):
sra.export(self._inv_obj, self._tmp_dir, sra_settings=self._sra_default_config)
actual_project_set_xml_obj = etree.fromstring(open(os.path.join(self._tmp_dir, 'project_set.xml'), 'rb').read())
self.assertTrue(utils.assert_xml_equal(self._expected_project_set_xml_obj, actual_project_set_xml_obj))