def test_magetab2json_convert_e_mexp_31(self):
actual_json = magetab2json.convert(
os.path.join(self._magetab_data_dir, 'E-MEXP-31.idf.txt'), )
with open(os.path.join(self._tmp_dir, 'isa.json'), 'w') as out_fp:
json.dump(actual_json, out_fp)
with open(os.path.join(self._tmp_dir, 'isa.json')) as actual_json:
report = isajson.validate(actual_json)
self.assertEqual(len(report['errors']), 0)
def test_magetab2json_convert_e_mexp_31(self):
with open(os.path.join(self._magetab_data_dir,
'E-MEXP-31.idf.txt')) as idf_fp:
actual_json = magetab2json.convert(idf_fp, 'protein microarray',
'protein expression profiling')
json.dump(actual_json,
open(os.path.join(self._tmp_dir, 'isa.json'), 'w'))
with open(os.path.join(self._tmp_dir, 'isa.json')) as actual_json:
report = isajson.validate(actual_json)
self.assertEqual(len(report['errors']), 0)
def getj(arrayexpress_id):
"""
This function downloads MAGE-TAB content as ISA-JSON from the ArrayExpress FTP site.
:param ax_experiment_id: Experiment identifier for ArrayExpress study to get, as a str (e.g. E-GEOD-59671)
:return: ISA-JSON representation of the MAGE-TAB content
Example usage:
from isatools.io import ax as AX
my_json = AX.getj('E-GEOD-59671')
"""
tmp_dir = tempfile.mkdtemp()
mage_json = None
try:
get(arrayexpress_id=arrayexpress_id, target_dir=tmp_dir)
mage_json = magetab2json.convert(os.path.join(tmp_dir, "{}.idf.txt".format(arrayexpress_id)))
except Exception as e:
log.fatal("Something went wrong: {}".format(e))
finally:
shutil.rmtree(tmp_dir)
return mage_json
