def create_links(gsrc, gdes, ctx):
# add soft and external links
srcid_desobj_map = ctx["srcid_desobj_map"]
if ctx["verbose"]:
print("create_links: {}".format(gsrc.name))
for title in gsrc:
msg = "got link: {}".format(title)
if ctx["verbose"]:
print(msg)
logging.info(msg)
lnk = gsrc.get(title, getlink=True)
link_classname = lnk.__class__.__name__
if link_classname == "HardLink":
logging.debug("Got hardlink: {} gsrc: {} gdes: {}".format(title, gsrc, gdes))
if title not in gdes:
msg = "creating link {} with title: {}".format(gdes, title)
if ctx["verbose"]:
print(msg)
logging.info(msg)
src_obj_id = gsrc[title].id
src_obj_id_hash = src_obj_id.__hash__()
logging.debug("got src_obj_id hash: {}".format(src_obj_id_hash))
if src_obj_id_hash in srcid_desobj_map:
des_obj = srcid_desobj_map[src_obj_id_hash]
logging.debug("creating hardlink to {}".format(des_obj.id.id))
gdes[title] = des_obj
else:
# TBD - in hdf5 1.10 it seems that two references to the same object
# can return different id's. This will cause HDF5 files with
# multilinks to not load correctly
msg = "could not find map item to src id: {}".format(src_obj_id_hash)
logging.warn(msg)
if ctx["verbose"]:
print("WARNING: " + msg)
elif link_classname == "SoftLink":
msg = "creating SoftLink({}) with title: {}".format(lnk.path, title)
if ctx["verbose"]:
print(msg)
logging.info(msg)
if is_h5py(gdes):
soft_link = h5py.SoftLink(lnk.path)
else:
soft_link = h5pyd.SoftLink(lnk.path)
gdes[title] = soft_link
elif link_classname == "ExternalLink":
msg = "creating ExternalLink({}, {}) with title: {}".format(lnk.filename, lnk.path, title)
if ctx["verbose"]:
print(msg)
logging.info(msg)
if is_h5py(gdes):
ext_link = h5py.ExternalLink(lnk.filename, lnk.path)
else:
ext_link = h5pyd.ExternalLink(lnk.filename, lnk.path)
gdes[title] = ext_link
else:
msg = "Unexpected link type: {}".format(lnk.__class__.__name__)
logging.warning(msg)
if ctx["verbose"]:
print(msg)
logging.info("flush fout")
def create_links(gsrc, gdes, ctx):
# add soft and external links
srcid_desobj_map = ctx["srcid_desobj_map"]
if ctx["verbose"]:
print("create_links: {}".format(gsrc.name))
for title in gsrc:
if ctx["verbose"]:
print("got link: {}".format(title))
lnk = gsrc.get(title, getlink=True)
link_classname = lnk.__class__.__name__
if link_classname == "HardLink":
logging.debug("Got hardlink: {} gsrc: {} gdes: {}".format(title, gsrc, gdes))
if title not in gdes:
msg = "creating multilink {} with title: {}".format(gdes, title)
if ctx["verbose"]:
print(msg)
logging.info(msg)
src_obj_id = gsrc[title].id
src_obj_id_hash = src_obj_id.__hash__()
logging.debug("got src_obj_id hash: {}".format(src_obj_id_hash))
if src_obj_id_hash in srcid_desobj_map:
des_obj = srcid_desobj_map[src_obj_id_hash]
logging.debug("creating hardlink to {}".format(des_obj.id.id))
gdes[title] = des_obj
else:
msg = "could not find map item to src id: {}".format(src_obj_id_hash)
logging.warn(msg)
if ctx["verbose"]:
print("WARNING: " + msg)
elif link_classname == "SoftLink":
msg = "creating SoftLink({}) with title: {}".format(lnk.path, title)
if ctx["verbose"]:
print(msg)
logging.info(msg)
if is_h5py(gdes):
soft_link = h5py.SoftLink(lnk.path)
else:
soft_link = h5pyd.SoftLink(lnk.path)
gdes[title] = soft_link
elif link_classname == "ExternalLink":
msg = "creating ExternalLink({}, {}) with title: {}".format(lnk.filename, lnk.path, title)
if ctx["verbose"]:
print(msg)
logging.info(msg)
if is_h5py(gdes):
ext_link = h5py.ExternalLink(lnk.filename, lnk.path)
else:
ext_link = h5pyd.ExternalLink(lnk.filename, lnk.path)
gdes[title] = ext_link
else:
msg = "Unexpected link type: {}".format(lnk.__class__.__name__)
logging.warning(msg)
if ctx["verbose"]:
print(msg)
def create_group(fd, gobj, verbose=False):
msg = "creating group {}".format(gobj.name)
logging.info(msg)
if verbose:
print(msg)
grp = fd.create_group(gobj.name)
# create attributes
for ga in gobj.attrs:
copy_attribute(grp, ga, gobj)
# create any soft/external links
for title in gobj:
lnk = gobj.get(title, getlink=True)
link_classname = lnk.__class__.__name__
if link_classname == "HardLink":
logging.debug("Got hardlink: {}".format(title))
# TBD: handle the case where multiple hardlinks point to same object
elif link_classname == "SoftLink":
msg = "creating SoftLink({}) with title: {}".format(
lnk.path, title)
if verbose:
print(msg)
logging.info(msg)
if is_h5py(fd):
soft_link = h5py.SoftLink(lnk.path)
else:
soft_link = h5pyd.SoftLink(lnk.path)
grp[title] = soft_link
elif link_classname == "ExternalLink":
msg = "creating ExternalLink({}, {}) with title: {}".format(
lnk.filename, lnk.path, title)
if verbose:
print(msg)
logging.info(msg)
if is_h5py(fd):
ext_link = h5py.ExternalLink(lnk.filename, lnk.path)
else:
ext_link = h5pyd.ExternalLink(lnk.filename, lnk.path)
grp[title] = ext_link
else:
msg = "Unexpected link type: {}".format(lnk.__class__.__name__)
logging.warning(msg)
if verbose:
print(msg)
def create_links(gsrc, gdes, ctx):
# add soft and external links
if ctx["verbose"]:
print("create_links: {}".format(gsrc.name))
for title in gsrc:
if ctx["verbose"]:
print("got link: {}".format(title))
lnk = gsrc.get(title, getlink=True)
link_classname = lnk.__class__.__name__
if link_classname == "HardLink":
logging.debug("Got hardlink: {}".format(title))
# TBD: handle the case where multiple hardlinks point to same object
elif link_classname == "SoftLink":
msg = "creating SoftLink({}) with title: {}".format(
lnk.path, title)
if ctx["verbose"]:
print(msg)
logging.info(msg)
if is_h5py(gdes):
soft_link = h5py.SoftLink(lnk.path)
else:
soft_link = h5pyd.SoftLink(lnk.path)
gdes[title] = soft_link
elif link_classname == "ExternalLink":
msg = "creating ExternalLink({}, {}) with title: {}".format(
lnk.filename, lnk.path, title)
if ctx["verbose"]:
print(msg)
logging.info(msg)
if is_h5py(gdes):
ext_link = h5py.ExternalLink(lnk.filename, lnk.path)
else:
ext_link = h5pyd.ExternalLink(lnk.filename, lnk.path)
gdes[title] = ext_link
else:
msg = "Unexpected link type: {}".format(lnk.__class__.__name__)
logging.warning(msg)
if ctx["verbose"]:
print(msg)
def test_create(self):
filename = "new_group." + self.base_domain
f = h5py.File(filename, 'w')
self.assertTrue(f.id.id is not None)
self.assertTrue('/' in f)
r = f['/']
self.assertEqual(len(r), 0)
self.assertTrue(isinstance(r, h5py.Group))
self.assertTrue(r.name, '/')
self.assertEqual(len(r.attrs.keys()), 0)
self.assertFalse('g1' in r)
r.create_group('g1')
self.assertTrue('g1' in r)
r.create_group('g2')
self.assertEqual(len(r), 2)
keys = []
# iterate through keys
for k in r:
keys.append(k)
self.assertEqual(len(keys), 2)
self.assertTrue('g1' in keys)
self.assertTrue('g2' in keys)
self.assertTrue('g1' in r)
self.assertTrue('/g1' in r)
g1 = r.get('/g1')
self.assertTrue(g1.id.id)
self.assertEqual(g1.name, '/g1')
g1_class = r.get('g1', getclass=True)
self.assertEqual(g1_class, h5py.Group)
# try creating a group that already exists
try:
r.create_group('g1')
self.assertTrue(False)
except ValueError:
pass # expected
r.create_group('g3')
self.assertEqual(len(r), 3)
del r['g3']
self.assertEqual(len(r), 2)
r.require_group('g4')
self.assertEqual(len(r), 3)
r.require_group('g2')
self.assertEqual(len(r), 3)
g1_1 = r.create_group("g1/g1.1")
self.assertEqual(len(r), 3)
self.assertEqual(len(g1), 1)
self.assertEqual(len(g1_1), 0)
# create a hardlink
r['g1.1'] = g1_1
self.assertEqual(len(r), 4)
# create a softlink
r['mysoftlink'] = h5py.SoftLink('/g1/g1.1')
self.assertEqual(len(r), 5)
#print r.get_link_json("/mysoftlink")
slink = r['mysoftlink']
self.assertEqual(slink.id, g1_1.id)
# create a external hardlink
r['myexternallink'] = h5py.ExternalLink("somefile", "somepath")
# test getclass
g1_class = r.get('g1', getclass=True)
self.assertEqual(g1_class, h5py.Group)
linkee_class = r.get('mysoftlink', getclass=True)
self.assertEqual(linkee_class, h5py.Group)
link_class = r.get('mysoftlink', getclass=True, getlink=True)
self.assertEqual(link_class, h5py.SoftLink)
softlink = r.get('mysoftlink', getlink=True)
self.assertEqual(softlink.path, '/g1/g1.1')
try:
linkee_class = r.get('myexternallink', getclass=True)
self.assertTrue(False)
except IOError:
pass # expected - not implemented
link_class = r.get('myexternallink', getclass=True, getlink=True)
self.assertEqual(link_class, h5py.ExternalLink)
external_link = r.get('myexternallink', getlink=True)
self.assertEqual(external_link.path, 'somepath')
del r['mysoftlink']
self.assertEqual(len(r), 5)
del r['myexternallink']
self.assertEqual(len(r), 4)
f.close()
self.assertEqual(f.id.id, 0)