def main():
parser = argparse.ArgumentParser(
usage='%(prog)s [-h] <json_file> <h5_file>')
parser.add_argument('in_filename',
nargs='+',
help='JSon file to be converted to h5')
parser.add_argument('out_filename',
nargs='+',
help='name of HDF5 output file')
args = parser.parse_args()
# create logger
log = logging.getLogger("h5serv")
# log.setLevel(logging.WARN)
log.setLevel(logging.INFO)
# add log handler
handler = logging.FileHandler('./jsontoh5.log')
# add handler to logger
log.addHandler(handler)
text = open(args.in_filename[0]).read()
# parse the json file
h5json = json.loads(text)
if "root" not in h5json:
raise Exception("no root key in input file")
root_uuid = h5json["root"]
filename = args.out_filename[0]
# create the file, will raise IOError if there's a problem
Hdf5db.createHDF5File(filename)
with Hdf5db(filename,
root_uuid=root_uuid,
update_timestamps=False,
app_logger=log) as db:
h5writer = Writeh5(db, h5json)
h5writer.writeFile()
# open with h5py and remove the _db_ group
# Note: this will delete any anonymous (un-linked) objects
f = h5py.File(filename, 'a')
if "__db__" in f:
del f["__db__"]
f.close()
print("done!")
def testReadCommittedType(self):
filepath = getFile('committed_type.h5', 'readcommitted_type.h5')
with Hdf5db(filepath, app_logger=self.log) as db:
root_uuid = db.getUUIDByPath('/')
type_uuid = db.getUUIDByPath('/Sensor_Type')
item = db.getCommittedTypeItemByUuid(type_uuid)
self.assertTrue('type' in item)
item_type = item['type']
self.assertTrue(item_type['class'], 'H5T_COMPOUND')
ds1_uuid = db.getUUIDByPath('/DS1')
item = db.getDatasetItemByUuid(ds1_uuid)
shape = item['shape']
self.failUnlessEqual(shape['class'], 'H5S_SIMPLE')
dims = shape['dims']
self.failUnlessEqual(len(dims), 1)
self.failUnlessEqual(dims[0], 4)
item_type = item['type']
self.assertTrue('class' in item_type)
self.failUnlessEqual(item_type['class'], 'H5T_COMPOUND')
self.assertTrue('uuid' in item_type)
self.failUnlessEqual(item_type['uuid'], type_uuid)
item = db.getAttributeItem("groups", root_uuid, "attr1") # FIXME: fails on Py3
shape = item['shape']
self.failUnlessEqual(shape['class'], 'H5S_SCALAR')
item_type = item['type']
self.assertTrue('class' in item_type)
self.failUnlessEqual(item_type['class'], 'H5T_COMPOUND')
self.assertTrue('uuid' in item_type)
self.failUnlessEqual(item_type['uuid'], type_uuid)
def testCreateVlenReferenceAttribute(self):
filepath = getFile('empty.h5', 'createreferenceattribute.h5')
with Hdf5db(filepath, app_logger=self.log) as db:
root_uuid = db.getUUIDByPath('/')
dims = () # if no space in body, default to scalar
rsp = db.createDataset("H5T_STD_I64LE", dims, max_shape=None, creation_props=None)
dset_uuid = rsp['id']
db.linkObject(root_uuid, dset_uuid, 'DS1')
dims = (1,)
datatype = {"class": "H5T_VLEN",
"base": { "class": "H5T_REFERENCE", "base": "H5T_STD_REF_OBJ"}
}
ds1_ref = "datasets/" + dset_uuid
value = [[ds1_ref,],]
db.createAttribute("groups", root_uuid, "A1", dims, datatype, value)
item = db.getAttributeItem("groups", root_uuid, "A1") # FIXME: fails on Py3
attr_type = item['type']
self.failUnlessEqual(attr_type["class"], "H5T_VLEN")
base_type = attr_type["base"]
# todo - this should be H5T_REFERENCE, not H5T_OPAQUE
# See h5py issue: https://github.com/h5py/h5py/issues/553
self.failUnlessEqual(base_type["class"], "H5T_OPAQUE")
def testWriteVlenUnicodeAttribute(self):
# getAttributeItemByUuid
item = None
filepath = getFile('empty.h5', 'writevlenunicodeattribute.h5')
with Hdf5db(filepath, app_logger=self.log) as db:
root_uuid = db.getUUIDByPath('/')
dims = ()
datatype = { 'charSet': 'H5T_CSET_UTF8',
'class': 'H5T_STRING',
'strPad': 'H5T_STR_NULLTERM',
'length': 'H5T_VARIABLE' }
value = u'\u6b22\u8fce\u63d0\u4ea4\u5fae\u535a\u641c\u7d22\u4f7f\u7528\u53cd\u9988\uff0c\u8bf7\u76f4\u63a5'
db.createAttribute("groups", root_uuid, "A1", dims, datatype, value)
item = db.getAttributeItem("groups", root_uuid, "A1") # FIXME: fails on Py3
self.failUnlessEqual(item['name'], "A1")
self.failUnlessEqual(item['value'], value)
now = int(time.time())
self.assertTrue(item['ctime'] > now - 5)
self.assertTrue(item['mtime'] > now - 5)
shape = item['shape']
self.failUnlessEqual(shape['class'], 'H5S_SCALAR')
item_type = item['type']
self.failUnlessEqual(item_type['class'], 'H5T_STRING')
self.failUnlessEqual(item_type['strPad'], 'H5T_STR_NULLTERM')
self.failUnlessEqual(item_type['charSet'], 'H5T_CSET_UTF8')
self.failUnlessEqual(item_type['length'], 'H5T_VARIABLE')
def testWriteVlenStringAttribute(self):
# getAttributeItemByUuid
item = None
filepath = getFile('empty.h5', 'writevlenstringattribute.h5')
with Hdf5db(filepath, app_logger=self.log) as db:
root_uuid = db.getUUIDByPath('/')
dims = ()
datatype = { 'charSet': 'H5T_CSET_ASCII',
'class': 'H5T_STRING',
'strPad': 'H5T_STR_NULLTERM',
'length': 'H5T_VARIABLE' }
value = "Hello, world!"
db.createAttribute("groups", root_uuid, "A1", dims, datatype, value) # FIXME: fails on Py3
item = db.getAttributeItem("groups", root_uuid, "A1")
self.failUnlessEqual(item['name'], "A1")
self.failUnlessEqual(item['value'], "Hello, world!")
now = int(time.time())
self.assertTrue(item['ctime'] > now - 5)
self.assertTrue(item['mtime'] > now - 5)
shape = item['shape']
self.failUnlessEqual(shape['class'], 'H5S_SCALAR')
item_type = item['type']
self.failUnlessEqual(item_type['class'], 'H5T_STRING')
self.failUnlessEqual(item_type['strPad'], 'H5T_STR_NULLTERM')
self.failUnlessEqual(item_type['charSet'], 'H5T_CSET_ASCII')
self.failUnlessEqual(item_type['length'], 'H5T_VARIABLE')
def testWriteFixedNullTermStringAttribute(self):
# getAttributeItemByUuid
item = None
filepath = getFile('empty.h5', 'writefixednulltermstringattribute.h5')
with Hdf5db(filepath, app_logger=self.log) as db:
root_uuid = db.getUUIDByPath('/')
dims = ()
datatype = { 'charSet': 'H5T_CSET_ASCII',
'class': 'H5T_STRING',
'strPad': 'H5T_STR_NULLTERM',
'length': 13}
value = "Hello, world!"
# write the attribute
db.createAttribute("groups", root_uuid, "A1", dims, datatype, value) # FIXME: fails on Py3
# read it back
item = db.getAttributeItem("groups", root_uuid, "A1")
self.failUnlessEqual(item['name'], "A1")
# the following compare fails - see issue #34
#self.failUnlessEqual(item['value'], "Hello, world!")
now = int(time.time())
self.assertTrue(item['ctime'] > now - 5)
self.assertTrue(item['mtime'] > now - 5)
shape = item['shape']
self.failUnlessEqual(shape['class'], 'H5S_SCALAR')
item_type = item['type']
self.failUnlessEqual(item_type['length'], 13)
self.failUnlessEqual(item_type['class'], 'H5T_STRING')
# NULLTERM get's converted to NULLPAD since the numpy dtype does not
# support other padding conventions.
self.failUnlessEqual(item_type['strPad'], 'H5T_STR_NULLPAD')
self.failUnlessEqual(item_type['charSet'], 'H5T_CSET_ASCII')
def testRootAcl(self):
filepath = getFile('tall.h5', 'rootacl.h5')
user1 = 123
with Hdf5db(filepath, app_logger=self.log) as db:
root_uuid = db.getUUIDByPath('/')
d111_uuid = db.getUUIDByPath('/g1/g1.1/dset1.1.1')
num_acls = db.getNumAcls(d111_uuid)
self.failUnlessEqual(num_acls, 0)
# add read/write acl for user1 at root
acl_root = db.getAcl(root_uuid, 0)
self.failUnlessEqual(acl_root['userid'], 0)
acl_root['create'] = 0
acl_root['read'] = 1
acl_root['update'] = 0
acl_root['delete'] = 0
acl_root['readACL'] = 0
acl_root['updateACL'] = 0
num_acls = db.getNumAcls(root_uuid)
self.failUnlessEqual(num_acls, 0)
db.setAcl(root_uuid, acl_root)
num_acls = db.getNumAcls(root_uuid)
self.failUnlessEqual(num_acls, 1)
acl = db.getAcl(d111_uuid, user1)
num_acls = db.getNumAcls(d111_uuid) # this will fetch the root acl
self.failUnlessEqual(num_acls, 0)
self.failUnlessEqual(acl['userid'], 0)
self.failUnlessEqual(acl['create'], 0)
self.failUnlessEqual(acl['read'], 1)
self.failUnlessEqual(acl['update'], 0)
self.failUnlessEqual(acl['delete'], 0)
self.failUnlessEqual(acl['readACL'], 0)
self.failUnlessEqual(acl['updateACL'], 0)
def testCreateCommittedCompoundTypeDataset(self):
filepath = getFile('empty.h5', 'createcommittedcompoundtypedataset.h5')
with Hdf5db(filepath, app_logger=self.log) as db:
root_uuid = db.getUUIDByPath('/')
datatype = {'class': 'H5T_COMPOUND',
'fields': [] }
type_fields = []
type_fields.append({'name': 'field_1', 'type': 'H5T_STD_I64BE' })
type_fields.append({'name': 'field_2', 'type': 'H5T_IEEE_F64BE' })
datatype['fields'] = type_fields
creation_props = {
"fillValue": [
0,
0.0 ]
}
item = db.createCommittedType(datatype) # FIXME: fails on Py3
type_uuid = item['id']
dims = () # if no space in body, default to scalar
rsp = db.createDataset(type_uuid, dims, max_shape=None, creation_props=creation_props)
dset_uuid = rsp['id']
item = db.getDatasetItemByUuid(dset_uuid)
type_item = item['type']
self.assertTrue('uuid' in type_item)
self.failUnlessEqual(type_item['uuid'], type_uuid)
def testGetNumLinks(self):
items = None
filepath = getFile('tall.h5', 'getnumlinks.h5')
with Hdf5db(filepath, app_logger=self.log) as db:
g1= db.getObjByPath('/g1')
numLinks = db.getNumLinksToObject(g1)
self.assertEqual(numLinks, 1)
def main():
parser = argparse.ArgumentParser(usage='%(prog)s [-h] [-D|-d] <hdf5_file>')
parser.add_argument('-D', action='store_true', help='surpress all data output')
parser.add_argument('-d', action='store_true', help='surpress data output for' +
' datasets (but not attribute values)')
parser.add_argument('filename', nargs='+', help='HDF5 to be converted to json')
args = parser.parse_args()
# create logger
log = logging.getLogger("h5serv")
# log.setLevel(logging.WARN)
log.setLevel(logging.INFO)
# add log handler
handler = logging.FileHandler('./h5tojson.log')
# add handler to logger
log.addHandler(handler)
filename = args.filename[0]
if not op.isfile(filename):
sys.exit("Cannot find file: %s" % filename)
log.info("h5tojson " + filename)
dbFilename = getTempFileName()
log.info("Using dbFile: " + dbFilename)
with Hdf5db(filename, dbFilePath=dbFilename, readonly=True, app_logger=log) as db:
dumper = DumpJson(db, app_logger=log, options=args)
dumper.dumpFile()
def testInvalidPath(self):
filepath = "/tmp/thisisnotafile.h5"
try:
with Hdf5db(filepath, app_logger=self.log) as db:
self.assertTrue(False) # shouldn't get here
except IOError as e:
self.failUnlessEqual(e.errno, errno.ENXIO)
self.failUnlessEqual(e.strerror, "file not found")
def testReadAttribute(self):
# getAttributeItemByUuid
item = None
filepath = getFile('tall.h5', 'readattribute.h5')
with Hdf5db(filepath, app_logger=self.log) as db:
rootUuid = db.getUUIDByPath('/')
self.failUnlessEqual(len(rootUuid), UUID_LEN)
item = db.getAttributeItem("groups", rootUuid, "attr1") # FIXME: fails on Py3
def testInvalidFile(self):
filepath = getFile('notahdf5file.h5', 'notahdf5file.h5')
try:
with Hdf5db(filepath, app_logger=self.log) as db:
self.assertTrue(False) # shouldn't get here
except IOError as e:
self.failUnlessEqual(e.errno, errno.EINVAL)
self.failUnlessEqual(e.strerror, "not an HDF5 file")
def main():
if len(sys.argv) < 2:
print "usage: h5tojson <filename>"
sys.exit()
filepath = sys.argv[1]
with Hdf5db(filepath, readonly=True) as db:
dumper = DumpJson(db)
dumper.dumpFile()
def testReadAttribute(self):
# getAttributeItemByUuid
item = None
getFile('tall.h5')
with Hdf5db('tall.h5') as db:
rootUuid = db.getUUIDByPath('/')
self.failUnlessEqual(len(rootUuid), config.get('uuidlen'))
item = db.getAttributeItem("groups", rootUuid, "attr1")
def testGetCounts(self):
with Hdf5db('tall.h5') as db:
cnt = db.getNumberOfGroups()
self.failUnlessEqual(cnt, 6)
cnt = db.getNumberOfDatasets()
self.failUnlessEqual(cnt, 4)
cnt = db.getNumberOfDatatypes()
self.failUnlessEqual(cnt, 0)
def testReadZeroDimDataset(self):
getFile('zerodim.h5')
d111_values = None
d112_values = None
with Hdf5db('zerodim.h5') as db:
dsetUuid = db.getUUIDByPath('/dset')
self.failUnlessEqual(len(dsetUuid), config.get('uuidlen'))
dset_value = db.getDatasetValuesByUuid(dsetUuid)
self.assertEqual(dset_value, 42)
def testReadZeroDimDataset(self):
filepath = getFile('zerodim.h5', 'readzerodeimdataset.h5')
d111_values = None
d112_values = None
with Hdf5db(filepath, app_logger=self.log) as db:
dsetUuid = db.getUUIDByPath('/dset')
self.failUnlessEqual(len(dsetUuid), UUID_LEN)
dset_value = db.getDatasetValuesByUuid(dsetUuid)
self.assertEqual(dset_value, 42)
def testGetCounts(self):
filepath = getFile('tall.h5', 'testgetcounts_tall.h5')
with Hdf5db(filepath, app_logger=self.log) as db:
cnt = db.getNumberOfGroups()
self.failUnlessEqual(cnt, 6)
cnt = db.getNumberOfDatasets()
self.failUnlessEqual(cnt, 4)
cnt = db.getNumberOfDatatypes()
self.failUnlessEqual(cnt, 0)
filepath = getFile('empty.h5', 'testgetcounts_empty.h5')
with Hdf5db(filepath, app_logger=self.log) as db:
cnt = db.getNumberOfGroups()
self.failUnlessEqual(cnt, 1)
cnt = db.getNumberOfDatasets()
self.failUnlessEqual(cnt, 0)
cnt = db.getNumberOfDatatypes()
self.failUnlessEqual(cnt, 0)
def testToTuple(self):
filepath = getFile('empty.h5', 'totuple.h5')
with Hdf5db(filepath, app_logger=self.log) as db:
self.assertEqual(db.toTuple( [1,2,3] ), (1,2,3) )
self.assertEqual(db.toTuple( [[1,2],[3,4]] ), ((1,2),(3,4)) )
self.assertEqual(db.toTuple( ([1,2],[3,4]) ), ((1,2),(3,4)) )
self.assertEqual(db.toTuple( [(1,2),(3,4)] ), ((1,2),(3,4)) )
self.assertEqual(db.toTuple( [[[1,2],[3,4]], [[5,6],[7,8]]] ),
(((1,2),(3,4)), ((5,6),(7,8))) )
def testDeleteLink(self):
# get test file
filepath = getFile('tall.h5', 'deletelink.h5')
with Hdf5db(filepath, app_logger=self.log) as db:
rootUuid = db.getUUIDByPath('/')
numRootChildren = len(db.getLinkItems(rootUuid))
self.assertEqual(numRootChildren, 2)
db.unlinkItem(rootUuid, "g2")
numRootChildren = len(db.getLinkItems(rootUuid))
self.assertEqual(numRootChildren, 1)
def testDeleteLink(self):
# get test file
getFile('tall.h5', 'tall_grpdelete.h5')
with Hdf5db('tall_grpdelete.h5') as db:
rootUuid = db.getUUIDByPath('/')
numRootChildren = len(db.getLinkItems(rootUuid))
self.assertEqual(numRootChildren, 2)
db.unlinkItem(rootUuid, "g2")
numRootChildren = len(db.getLinkItems(rootUuid))
self.assertEqual(numRootChildren, 1)
def testGetItemSoftLink(self):
with Hdf5db('tall.h5') as db:
grpUuid = db.getUUIDByPath('/g1/g1.2/g1.2.1')
item = db.getLinkItemByUuid(grpUuid, "slink")
self.assertTrue('id' not in item)
self.assertEqual(item['title'], 'slink')
self.assertEqual(item['class'], 'H5L_TYPE_SOFT')
self.assertEqual(item['h5path'], 'somevalue')
self.assertTrue('mtime' in item)
self.assertTrue('ctime' in item)
def main():
parser = argparse.ArgumentParser(usage='%(prog)s [-h] <json_file> <h5_file>')
parser.add_argument('in_filename', nargs='+', help='JSon file to be converted to h5')
parser.add_argument('out_filename', nargs='+', help='name of HDF5 output file')
args = parser.parse_args()
# create logger
log = logging.getLogger("h5serv")
# log.setLevel(logging.WARN)
log.setLevel(logging.INFO)
# add log handler
handler = logging.FileHandler('./jsontoh5.log')
# add handler to logger
log.addHandler(handler)
text = open(args.in_filename[0]).read()
# parse the json file
h5json = json.loads(text)
if "root" not in h5json:
raise Exception("no root key in input file")
root_uuid = h5json["root"]
filename = args.out_filename[0]
# create the file, will raise IOError if there's a problem
Hdf5db.createHDF5File(filename)
with Hdf5db(filename, root_uuid=root_uuid, update_timestamps=False, app_logger=log) as db:
h5writer = Writeh5(db, h5json)
h5writer.writeFile()
# open with h5py and remove the _db_ group
# Note: this will delete any anonymous (un-linked) objects
f = h5py.File(filename, 'a')
if "__db__" in f:
del f["__db__"]
f.close()
print("done!")
def testGetItemHardLink(self):
with Hdf5db('tall.h5') as db:
grpUuid = db.getUUIDByPath('/g1/g1.1')
item = db.getLinkItemByUuid(grpUuid, "dset1.1.1")
self.assertTrue('id' in item)
self.assertEqual(item['title'], 'dset1.1.1')
self.assertEqual(item['class'], 'H5L_TYPE_HARD')
self.assertEqual(item['collection'], 'datasets')
self.assertTrue('target' not in item)
self.assertTrue('mtime' in item)
self.assertTrue('ctime' in item)
def testDeleteUDLink(self):
# get test file
getFile('tall_with_udlink.h5')
with Hdf5db('tall_with_udlink.h5') as db:
g2Uuid = db.getUUIDByPath('/g2')
numG2Children = len(db.getLinkItems(g2Uuid))
self.assertEqual(numG2Children, 3)
rc = db.unlinkItem(g2Uuid, "udlink")
self.assertFalse(rc)
numG2Children = len(db.getLinkItems(g2Uuid))
self.assertEqual(numG2Children, 3)
def testGetItemHardLink(self):
with Hdf5db('tall.h5') as db:
grpUuid = db.getUUIDByPath('/g1/g1.1')
item = db.getLinkItemByUuid(grpUuid, "dset1.1.1")
self.assertTrue('id' in item)
self.assertEqual(item['name'], 'dset1.1.1')
self.assertEqual(item['class'], 'hard')
self.assertEqual(item['className'], 'Dataset')
self.assertTrue('target' not in item)
self.assertTrue('mtime' in item)
self.assertTrue('ctime' in item)
def testGetUUIDByPath(self):
# get test file
g1Uuid = None
with Hdf5db('tall.h5') as db:
g1Uuid = db.getUUIDByPath('/g1')
self.failUnlessEqual(len(g1Uuid), config.get('uuidlen'))
obj = db.getObjByPath('/g1')
self.failUnlessEqual(obj.name, '/g1')
for name in obj:
g = obj[name]
g1links = db.getLinkItems(g1Uuid)
self.failUnlessEqual(len(g1links), 2)
for item in g1links:
self.failUnlessEqual(len(item['id']), config.get('uuidlen'))
# end of with will close file
# open again and verify we can get obj by name
with Hdf5db('tall.h5') as db:
obj = db.getGroupObjByUuid(g1Uuid)
g1 = db.getObjByPath('/g1')
self.failUnlessEqual(obj, g1)
def testGetItemExternalLink(self):
getFile('tall_with_udlink.h5')
with Hdf5db('tall_with_udlink.h5') as db:
grpUuid = db.getUUIDByPath('/g1/g1.2')
item = db.getLinkItemByUuid(grpUuid, "extlink")
self.assertTrue('uuid' not in item)
self.assertEqual(item['title'], 'extlink')
self.assertEqual(item['class'], 'H5L_TYPE_EXTERNAL')
self.assertEqual(item['h5path'], 'somepath')
self.assertEqual(item['file'], 'somefile')
self.assertTrue('mtime' in item)
self.assertTrue('ctime' in item)
def testGetItemUDLink(self):
getFile('tall_with_udlink.h5')
with Hdf5db('tall_with_udlink.h5') as db:
grpUuid = db.getUUIDByPath('/g2')
item = db.getLinkItemByUuid(grpUuid, "udlink")
self.assertTrue('uuid' not in item)
self.assertEqual(item['title'], 'udlink')
self.assertEqual(item['class'], 'H5L_TYPE_USER_DEFINED')
self.assertTrue('h5path' not in item)
self.assertTrue('file' not in item)
self.assertTrue('mtime' in item)
self.assertTrue('ctime' in item)
def testReadOnlyGetUUID(self):
# get test file
getFile('tall.h5', 'tall_ro.h5', True)
# remove db file!
removeFile('.tall_ro.h5')
g1Uuid = None
with Hdf5db('tall_ro.h5') as db:
g1Uuid = db.getUUIDByPath('/g1')
self.failUnlessEqual(len(g1Uuid), config.get('uuidlen'))
obj = db.getObjByPath('/g1')
self.failUnlessEqual(obj.name, '/g1')
# end of with will close file
# open again and verify we can get obj by name
with Hdf5db('tall_ro.h5') as db:
obj = db.getGroupObjByUuid(g1Uuid)
g1 = db.getObjByPath('/g1')
self.failUnlessEqual(obj, g1)
g1links = db.getLinkItems(g1Uuid)
self.failUnlessEqual(len(g1links), 2)
for item in g1links:
self.failUnlessEqual(len(item['id']), config.get('uuidlen'))
def main():
nargs = len(sys.argv)
dumper = Dumph5()
dumper.verbose = False
dumper.endpoint = None
dumper.port = 7253
dumper.noDsetData = False
dumper.noAttrData = False
endpoint_option = "-endpoint="
port_option = "-port="
option_count = 0
for arg in sys.argv:
if arg.startswith(endpoint_option):
endpoint = arg[len(endpoint_option):]
if endpoint.startswith("http"):
dumper.endpoint = endpoint
else:
dumper.endpoint = "http://" + endpoint
option_count += 1
elif arg.startswith(port_option):
port = arg[len(port_option):]
dumper.port = int(port)
option_count += 1
elif arg == "-v":
dumper.verbose = True
if nargs - option_count <= 2:
printUsage()
domain = sys.argv[nargs-2]
filename = sys.argv[nargs-1]
print "domain:", domain
print "filename:", filename
dumper.domain = domain
domain_json = dumper.makeRequest("/")
if "root" not in domain_json:
raise Exception("no root key in domain response")
root_uuid = domain_json["root"]
# create the file, will raise IOError if there's a problem
Hdf5db.createHDF5File(filename)
with Hdf5db(filename, root_uuid=root_uuid) as db:
dumper.writeFile(db)
# open with h5py and remove the _db_ group
# Note: this will delete any anonymous (un-linked) objects
f = h5py.File(filename, 'a')
del f["__db__"]
f.close()
print "done!"