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

- Enable testing for this path

 - Fixes #1166
 - Fixes #1167
 - Fixes #1168

server/data_common/data_adaptor.py

@@ -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:

server/data_cxg/cxg_adaptor.py

@@ -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:
+            if axis == Axis.OBS:
-                try:
+                if labels is not None and not labels.empty:
-                    df = pd.DataFrame(A.query(attrs=fields)[:])
+                    df = pd.DataFrame.from_dict(A[:])
-                except tiledb.libtiledb.TileDBError:
+                    df = df.join(labels, self.get_obs_names())
-                    raise KeyError("bad field {fields}")
+                else:
-
+                    df = pd.DataFrame.from_dict(A[:])
             else:
                 df = pd.DataFrame.from_dict(A[:])
 
-            if axis == Axis.OBS:
+            if fields is not None and len(fields) > 0:
-                if labels is not None and not labels.empty:
+                df = df[fields]
-                    obs_names = self.get_obs_names()
-                    df = df.join(labels, obs_names)
 
         with ServerTiming.time(f"annotations.{axis}.encode"):
             fbs = encode_matrix_fbs(df, col_idx=df.columns)

server/test/test_api.py

@@ -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"