def convert(json_fp, path, config_dir=None):
""" 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
"""
from isatools.convert import json2isatab, isatab2sra
json2isatab.convert(json_fp=json_fp, path=path, config_dir=config_dir)
isatab2sra.create_sra(path, path)
for f in glob(path + '/*.txt'): # remove generated isatab files
os.remove(f)
def post(self):
response = Response(status=500)
# Create temporary directory
tmp_dir = _create_temp_dir()
try:
if tmp_dir is None:
raise IOError("Could not create temporary directory " + tmp_dir)
if not request.mimetype == "application/zip":
raise TypeError("Incorrect media type received. Got " + request.mimetype + ", expected application/zip")
else:
# Write request data to file
file_path = _write_request_data(request, tmp_dir, 'isatab.zip')
if file_path is None:
raise IOError("Could not create temporary file " + file_path)
# Setup path to configuration
config_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'isaconfig-default')
with zipfile.ZipFile(file_path, 'r') as z:
# extract ISArchive files
z.extractall(tmp_dir)
src_dir = os.path.normpath(os.path.join(tmp_dir, z.filelist[0].filename))
# convert to SRA writes to /sra
isatab2sra.create_sra(src_dir, tmp_dir, config_dir)
memf = io.BytesIO()
with zipfile.ZipFile(memf, 'w') as zf:
for file in os.listdir(tmp_dir + '/sra/' + z.filelist[0].filename):
zf.write(os.path.join(tmp_dir + '/sra/' + z.filelist[0].filename, file), file)
memf.seek(0)
response = send_file(memf, mimetype='application/zip')
except TypeError:
response = Response(status=415)
except Exception:
response = Response(status=500)
finally:
shutil.rmtree(tmp_dir, ignore_errors=True)
return response
def test_isatab_to_sra(self):
from isatools.convert import isatab2sra
isatab2sra.create_sra(self._work_dir, self._sra_dir, self._config_dir)
assert (os.path.exists(os.path.join(self._sra_dir, "/sra")), True)