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BUG: Presence of softlink in HDF5 file breaks HDFStore.keys() (GH20523) #20537

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Merged
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Apr 3, 2018
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BUG: Presence of softlink in HDF5 file breaks HDFStore.keys() (GH20523) #20537

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1 change: 1 addition & 0 deletions doc/source/whatsnew/v0.23.0.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -1098,6 +1098,7 @@ I/O
- Bug in :func:`read_pickle` when unpickling objects with :class:`TimedeltaIndex` or :class:`Float64Index` created with pandas prior to version 0.20 (:issue:`19939`)
- Bug in :meth:`pandas.io.json.json_normalize` where subrecords are not properly normalized if any subrecords values are NoneType (:issue:`20030`)
- Bug in ``usecols`` parameter in :func:`pandas.io.read_csv` and :func:`pandas.io.read_table` where error is not raised correctly when passing a string. (:issue:`20529`)
- Bug in :func:`HDFStore.keys` when reading a file with a softlink causes exception (:issue:`20523`)

Plotting
^^^^^^^^
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7 changes: 4 additions & 3 deletions pandas/io/pytables.py
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Expand Up @@ -1073,10 +1073,11 @@ def groups(self):
self._check_if_open()
return [
g for g in self._handle.walk_nodes()
if (getattr(g._v_attrs, 'pandas_type', None) or
getattr(g, 'table', None) or
if (not isinstance(g, _table_mod.link.Link) and
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Are there any other cases we should exclude, or just Link?

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Link is the abstract base class for SoftLink and ExternalLink in pytables. These subclasses do not support attributes as of HDF5 (this appears to be a limitation of the HDF5 library but may change in the future, reference: http://www.pytables.org/usersguide/libref/link_classes.html). I believe all other node types support attributes. A quick search of NoAttrs in Pytables shows usage only in tables/link.py.

(getattr(g._v_attrs, 'pandas_type', None) or
getattr(g, 'table', None) or
(isinstance(g, _table_mod.table.Table) and
g._v_name != u('table')))
g._v_name != u('table'))))
]

def get_node(self, key):
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17 changes: 17 additions & 0 deletions pandas/tests/io/test_pytables.py
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Expand Up @@ -373,6 +373,23 @@ def test_keys(self):
assert set(store.keys()) == expected
assert set(store) == expected

def test_keys_ignore_hdf_softlink(self):

# GH 20523
# Puts a softlink into HDF file and rereads

with ensure_clean_store(self.path) as store:

df = DataFrame(dict(A=lrange(5), B=lrange(5)))
store.put("df", df)

assert store.keys() == ["/df"]

store._handle.create_soft_link(store._handle.root, "symlink", "df")

# Should ignore the softlink
assert store.keys() == ["/df"]

def test_iter_empty(self):

with ensure_clean_store(self.path) as store:
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