Swap shared_ptr with const reference, hide internal columns when open…

…ing an array for read unless explicity specify them
single-cell-data · Nov 1, 2024 · eb47db2 · eb47db2
1 parent fbac212
commit eb47db2
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Showing 4 changed files with 24 additions and 41 deletions.
diff --git a/libtiledbsoma/src/soma/soma_array.cc b/libtiledbsoma/src/soma/soma_array.cc
@@ -250,6 +250,25 @@ void SOMAArray::reset(
 
     if (!column_names.empty()) {
         mq_->select_columns(column_names);
+    } else {
+        // Hide internal columns if any
+        std::vector<std::string> columns;
+        for (const auto& dim : this->tiledb_schema()->domain().dimensions()) {
+            columns.push_back(dim.name());
+        }
+
+        for (size_t i = 0; i < this->tiledb_schema()->attribute_num(); ++i) {
+            columns.push_back(this->tiledb_schema()->attribute(i).name());
+        }
+        auto is_internal = [](std::string name) {
+            return name.rfind(SOMA_GEOMETRY_DIMENSION_PREFIX, 0) == 0;
+        };
+
+        auto internal_end = std::remove_if(
+            columns.begin(), columns.end(), is_internal);
+        columns.erase(internal_end, columns.end());
+
+        mq_->select_columns(columns);
     }
 
     switch (result_order) {

diff --git a/libtiledbsoma/src/utils/arrow_adapter.cc b/libtiledbsoma/src/utils/arrow_adapter.cc
@@ -392,7 +392,7 @@ std::unique_ptr<ArrowSchema> ArrowAdapter::arrow_schema_from_tiledb_array(
                 } else if constexpr (std::is_same_v<T, Attribute>) {
                     child = arrow_schema->children[i] =
                         arrow_schema_from_tiledb_attribute(
-                            arg, ctx, tiledb_array)
+                            arg, *ctx, *tiledb_array)
                             .release();
                 }
             },
@@ -425,9 +425,7 @@ std::unique_ptr<ArrowSchema> ArrowAdapter::arrow_schema_from_tiledb_dimension(
 }
 
 std::unique_ptr<ArrowSchema> ArrowAdapter::arrow_schema_from_tiledb_attribute(
-    Attribute& attribute,
-    std::shared_ptr<Context> ctx,
-    std::shared_ptr<Array> tiledb_array) {
+    Attribute& attribute, const Context& ctx, const Array& tiledb_array) {
     std::unique_ptr<ArrowSchema> arrow_schema = std::make_unique<ArrowSchema>();
     arrow_schema->format = strdup(
         ArrowAdapter::to_arrow_format(attribute.type()).data());
@@ -454,10 +452,10 @@ std::unique_ptr<ArrowSchema> ArrowAdapter::arrow_schema_from_tiledb_attribute(
         arrow_schema->name));
 
     auto enmr_name = AttributeExperimental::get_enumeration_name(
-        *ctx, attribute);
+        ctx, attribute);
     if (enmr_name.has_value()) {
         auto enmr = ArrayExperimental::get_enumeration(
-            *ctx, *tiledb_array, attribute.name());
+            ctx, tiledb_array, attribute.name());
         auto dict = (ArrowSchema*)malloc(sizeof(ArrowSchema));
         dict->format = strdup(
             ArrowAdapter::to_arrow_format(enmr.type(), false).data());

diff --git a/libtiledbsoma/src/utils/arrow_adapter.h b/libtiledbsoma/src/utils/arrow_adapter.h
@@ -243,9 +243,7 @@ class ArrowAdapter {
      * @return ArrowSchema
      */
     static std::unique_ptr<ArrowSchema> arrow_schema_from_tiledb_attribute(
-        Attribute& attribute,
-        std::shared_ptr<Context> ctx,
-        std::shared_ptr<Array> tiledb_array);
+        Attribute& attribute, const Context& ctx, const Array& tiledb_array);
 
     /**
      * @brief Get members of the TileDB Schema in the form of a PlatformConfig

diff --git a/libtiledbsoma/test/unit_soma_geometry_dataframe.cc b/libtiledbsoma/test/unit_soma_geometry_dataframe.cc
@@ -313,43 +313,11 @@ TEST_CASE("SOMAGeometryDataFrame: Roundtrip", "[SOMAGeometryDataFrame]") {
         while (auto batch = soma_geometry->read_next()) {
             auto arrbuf = batch.value();
             auto d0span = arrbuf->at(dim_infos[0].name)->data<int64_t>();
-            auto d1span = arrbuf
-                              ->at(
-                                  SOMA_GEOMETRY_DIMENSION_PREFIX +
-                                  spatial_dim_infos[0].name + "__min")
-                              ->data<double_t>();
-            auto d2span = arrbuf
-                              ->at(
-                                  SOMA_GEOMETRY_DIMENSION_PREFIX +
-                                  spatial_dim_infos[0].name + "__max")
-                              ->data<double_t>();
-            auto d3span = arrbuf
-                              ->at(
-                                  SOMA_GEOMETRY_DIMENSION_PREFIX +
-                                  spatial_dim_infos[1].name + "__min")
-                              ->data<double_t>();
-            auto d4span = arrbuf
-                              ->at(
-                                  SOMA_GEOMETRY_DIMENSION_PREFIX +
-                                  spatial_dim_infos[1].name + "__max")
-                              ->data<double_t>();
             auto wkbs = arrbuf->at(dim_infos[1].name)->binaries();
             auto a0span = arrbuf->at(attr_infos[0].name)->data<double>();
             CHECK(
                 std::vector<int64_t>({1}) ==
                 std::vector<int64_t>(d0span.begin(), d0span.end()));
-            CHECK(
-                std::vector<double_t>({0}) ==
-                std::vector<double_t>(d1span.begin(), d1span.end()));
-            CHECK(
-                std::vector<double_t>({1}) ==
-                std::vector<double_t>(d2span.begin(), d2span.end()));
-            CHECK(
-                std::vector<double_t>({0}) ==
-                std::vector<double_t>(d3span.begin(), d3span.end()));
-            CHECK(
-                std::vector<double_t>({1}) ==
-                std::vector<double_t>(d4span.begin(), d4span.end()));
             CHECK(geometry::to_wkb(polygon) == wkbs[0]);
             CHECK(
                 std::vector<double_t>({63}) ==