fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-09-30 22:48:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

Fix various bugs with CXG format at annotations (#1173)

Browse Source 
- Enable testing for this path

 - Fixes #1166
 - Fixes #1167
 - Fixes #1168
This commit is contained in:
bmccandless
2020-02-24 18:19:39 -08:00
committed by GitHub
parent 7bc58bba2b
commit 46876e2fb1
3 changed files with 11 additions and 18 deletions
Download Patch File Download Diff File Expand all files Collapse all files
server/data_cxg/cxg_adaptor.py
+8 -10
View File
@@ -292,19 +292,17 @@ class CxgAdaptor(DataAdaptor):
def annotation_to_fbs_matrix(self, axis, fields=None, labels=None):
with ServerTiming.time(f"annotations.{axis}.query"):
A = self.open_array(str(axis))
if fields is not None and len(fields) > 0:
try:
df = pd.DataFrame(A.query(attrs=fields)[:])
except tiledb.libtiledb.TileDBError:
raise KeyError("bad field {fields}")
if axis == Axis.OBS:
if labels is not None and not labels.empty:
df = pd.DataFrame.from_dict(A[:])
df = df.join(labels, self.get_obs_names())
else:
df = pd.DataFrame.from_dict(A[:])
else:
df = pd.DataFrame.from_dict(A[:])
if axis == Axis.OBS:
if labels is not None and not labels.empty:
obs_names = self.get_obs_names()
df = df.join(labels, obs_names)
if fields is not None and len(fields) > 0:
df = df[fields]
with ServerTiming.time(f"annotations.{axis}.encode"):
fbs = encode_matrix_fbs(df, col_idx=df.columns)