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

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- 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
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2
server/data_common/data_adaptor.py
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@@ -213,6 +213,8 @@ class DataAdaptor(metaclass=ABCMeta):
return
labels_df.index = self.get_obs_index()
if labels_df.index.name is None:
labels_df.index.name = "index"
# all labels must have a name, which must be unique and not used in obs column names
if not labels_df.columns.is_unique:

18
server/data_cxg/cxg_adaptor.py
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)

9
server/test/test_api.py
View File

@@ -8,13 +8,12 @@ import pandas as pd
import requests
import server.test.decode_fbs as decode_fbs
from server.test import skip_if, data_with_tmp_annotations, make_fbs
from server.test import data_with_tmp_annotations, make_fbs
from server.data_common.matrix_loader import MatrixDataType
BAD_FILTER = {"filter": {"obs": {"annotation_value": [{"name": "xyz"}]}}}
# TODO (mweiden): remove ANNOTATIONS_ENABLED and Annotation subclasses when annotations are no longer experimental
# TODO (mweiden): remove MATRIX_DATA_TYPE and skip_if when user annotations for the CXG format is complete
class EndPoints(object):
@@ -91,10 +90,6 @@ class EndPoints(object):
+ (["cluster-test"] if self.ANNOTATIONS_ENABLED else []),
)
@skip_if(
lambda slf: hasattr(slf, "MATRIX_DATA_TYPE") and slf.MATRIX_DATA_TYPE == MatrixDataType.CXG,
"CXG file annotations are not feature-complete!",
)
def test_get_annotations_obs_keys_fbs(self):
endpoint = "annotations/obs"
query = "annotation-name=n_genes&annotation-name=percent_mito"
@@ -275,13 +270,11 @@ class EndPointsAnnotations(EndPoints):
def test_get_schema_existing_writable(self):
self._test_get_schema_writable("cluster-test")
@skip_if(lambda slf: slf.MATRIX_DATA_TYPE == MatrixDataType.CXG, "CXG file annotations are not feature-complete!")
def test_get_user_annotations_existing_obs_keys_fbs(self):
self._test_get_user_annotations_obs_keys_fbs(
"cluster-test", {"unassigned", "one", "two", "three", "four", "five"},
)
@skip_if(lambda slf: slf.MATRIX_DATA_TYPE == MatrixDataType.CXG, "CXG file annotations are not feature-complete!")
def test_put_user_annotations_obs_fbs(self):
endpoint = "annotations/obs"
query = "annotation-collection-name=test_annotations"