fix: upgraded tiledb and reverted workaround (#61) (#66)

chanzuckerberg · Sep 17, 2021 · 6841c72 · 6841c72
1 parent 055a64d
commit 6841c72
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Showing 3 changed files with 4 additions and 22 deletions.
diff --git a/server/compute/diffexp_cxg.py b/server/compute/diffexp_cxg.py
@@ -87,24 +87,11 @@ def diffexp_ttest(adaptor, maskA, maskB, top_n=8, diffexp_lfc_cutoff=0.01):
 
     if is_sparse:
         for cols in col_partitions:
-            futures.append(
-                executor.submit(
-                    # TODO: remove this temporary workaround when TileDB fixes the issue with multi_index
-                    _mean_var_sparse_ab, adaptor.open_array("X"), row_selector_A, nA, row_selector_B, nB, cols
-                )
-            )
+            futures.append(executor.submit(_mean_var_sparse_ab, matrix, row_selector_A, nA, row_selector_B, nB, cols))
     else:
         for cols in col_partitions:
             futures.append(
-                executor.submit(
-                    _mean_var_ab,
-                    # TODO: remove this temporary workaround when TileDB fixes the issue with multi_index
-                    adaptor.open_array("X"),
-                    row_selector_AB,
-                    row_selector_A_in_AB,
-                    row_selector_B_in_AB,
-                    cols,
-                )
+                executor.submit(_mean_var_ab, matrix, row_selector_AB, row_selector_A_in_AB, row_selector_B_in_AB, cols)
             )
 
     for future in futures:

diff --git a/server/data_cxg/cxg_adaptor.py b/server/data_cxg/cxg_adaptor.py
@@ -195,12 +195,7 @@ def _open_array(uri, tiledb_ctx):
     def open_array(self, name):
         try:
             p = self.get_path(name)
-            # TODO: remove this temporary workaround when TileDB fixes the issue with multi_index
-            if name == "X" or name == "X_col_shift":
-                # workaround: bypass the cache for arrays that use multi_index
-                return CxgAdaptor._open_array(p, self.tiledb_ctx)
-            else:
-                return self.arrays[p]
+            return self.arrays[p]
         except tiledb.libtiledb.TileDBError:
             raise DatasetAccessError(name)
 

diff --git a/server/requirements.txt b/server/requirements.txt
@@ -19,6 +19,6 @@ pandas>=1.0,!=1.1  # pandas 1.1 breaks tests, https://github.com/pandas-dev/pand
 PyYAML>=5.4  # CVE-2020-14343
 scipy>=1.4
 requests>=2.22.0
-tiledb==0.10.0
+tiledb==0.10.1
 s3fs==0.4.2
 sqlalchemy>=1.3.18