[c++] Column abstraction: SOMAAttribute, part 2 (#3426)

* Add concrete class wrapper for TileDB attribute * Misc fixes * Add missing `override` * Remove current_domain flag * Replace string_view with string when returning column name, add current domain checks, replace vector with span when selecting points * Update CMake files * Add description and license * Address review comments * Comply with C.128 * Update libtiledbsoma/src/soma/soma_attribute.cc Co-authored-by: Julia Dark <[email protected]> * Update libtiledbsoma/src/soma/soma_attribute.h Co-authored-by: Julia Dark <[email protected]> --------- Co-authored-by: Julia Dark <[email protected]>
single-cell-data · Jan 3, 2025 · c5ed9da · c5ed9da
1 parent 9e7a461
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diff --git a/libtiledbsoma/src/CMakeLists.txt b/libtiledbsoma/src/CMakeLists.txt
@@ -34,6 +34,7 @@ add_library(TILEDB_SOMA_OBJECTS OBJECT
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_group.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_object.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_column.cc
+  ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_attribute.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_dimension.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_collection.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_experiment.cc
@@ -209,6 +210,7 @@ install(FILES
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_array.h
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_group.h
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_column.h
+  ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_attribute.h
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_dimension.h
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_collection.h
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_dataframe.h

diff --git a/libtiledbsoma/src/soma/soma_attribute.cc b/libtiledbsoma/src/soma/soma_attribute.cc
@@ -0,0 +1,127 @@
+/**
+ * @file   soma_attribute.cc
+ *
+ * @section LICENSE
+ *
+ * The MIT License
+ *
+ * @copyright Copyright (c) 2024-2025 TileDB, Inc.
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ *
+ * @section DESCRIPTION
+ *
+ *   This file defines the SOMAAttribute class.
+ */
+
+#include "soma_attribute.h"
+
+namespace tiledbsoma {
+std::shared_ptr<SOMAAttribute> SOMAAttribute::create(
+    std::shared_ptr<Context> ctx,
+    ArrowSchema* schema,
+    std::string_view type_metadata,
+    PlatformConfig platform_config) {
+    auto attribute = ArrowAdapter::tiledb_attribute_from_arrow_schema(
+        ctx, schema, type_metadata, platform_config);
+
+    return std::make_shared<SOMAAttribute>(
+        SOMAAttribute(attribute.first, attribute.second));
+}
+
+void SOMAAttribute::_set_dim_points(
+    const std::unique_ptr<ManagedQuery>&,
+    const SOMAContext&,
+    const std::any&) const {
+    throw TileDBSOMAError(std::format(
+        "[SOMAAttribute][_set_dim_points] Column with name {} is not an index "
+        "column",
+        name()));
+}
+
+void SOMAAttribute::_set_dim_ranges(
+    const std::unique_ptr<ManagedQuery>&,
+    const SOMAContext&,
+    const std::any&) const {
+    throw TileDBSOMAError(std::format(
+        "[SOMAAttribute][_set_dim_ranges] Column with name {} is not an index "
+        "column",
+        name()));
+}
+
+void SOMAAttribute::_set_current_domain_slot(
+    NDRectangle&, std::span<const std::any>) const {
+    throw TileDBSOMAError(std::format(
+        "[SOMAAttribute][_set_current_domain_slot] Column with name {} is not "
+        "an index column",
+        name()));
+}
+
+std::pair<bool, std::string> SOMAAttribute::_can_set_current_domain_slot(
+    std::optional<NDRectangle>&, std::span<const std::any>) const {
+    throw TileDBSOMAError(std::format(
+        "[SOMAAttribute][_set_current_domain_slot] Column with name {} is not "
+        "an index column",
+        name()));
+};
+
+std::any SOMAAttribute::_core_domain_slot() const {
+    throw TileDBSOMAError(std::format(
+        "[SOMAAttribute][_core_domain_slot] Column with name {} is not an "
+        "index column",
+        name()));
+}
+
+std::any SOMAAttribute::_non_empty_domain_slot(Array&) const {
+    throw TileDBSOMAError(std::format(
+        "[SOMAAttribute][_non_empty_domain_slot] Column with name {} is not an "
+        "index column",
+        name()));
+}
+
+std::any SOMAAttribute::_core_current_domain_slot(
+    const SOMAContext&, Array&) const {
+    throw TileDBSOMAError(std::format(
+        "[SOMAAttribute][_core_current_domain_slot] Column with name {} is not "
+        "an index column",
+        name()));
+}
+
+std::any SOMAAttribute::_core_current_domain_slot(NDRectangle&) const {
+    throw TileDBSOMAError(std::format(
+        "[SOMAAttribute][_core_current_domain_slot] Column with name {} is not "
+        "an index column",
+        name()));
+}
+
+ArrowArray* SOMAAttribute::arrow_domain_slot(
+    const SOMAContext&, Array&, enum Domainish) const {
+    throw TileDBSOMAError(std::format(
+        "[SOMAAttribute][arrow_domain_slot] Column with name {} is not an "
+        "index column",
+        name()));
+}
+
+ArrowSchema* SOMAAttribute::arrow_schema_slot(
+    const SOMAContext& ctx, Array& array) {
+    return ArrowAdapter::arrow_schema_from_tiledb_attribute(
+               attribute, *ctx.tiledb_ctx(), array)
+        .release();
+}
+}  // namespace tiledbsoma
diff --git a/libtiledbsoma/src/soma/soma_attribute.h b/libtiledbsoma/src/soma/soma_attribute.h
@@ -0,0 +1,150 @@
+/**
+ * @file   soma_attribute.h
+ *
+ * @section LICENSE
+ *
+ * The MIT License
+ *
+ * @copyright Copyright (c) 2024-2025 TileDB, Inc.
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ *
+ * @section DESCRIPTION
+ *
+ *   This file defines the SOMAAttribute class. SOMAAttribute extends SOMAColumn
+ * and wraps a TileDB Attribute and optionally an enumeration associated with
+ * the attribute. The purpose of this class is to provide a common interface
+ * identical to TileDB dimensions and composite columns.
+ */
+
+#ifndef SOMA_ATTRIBUTE_H
+#define SOMA_ATTRIBUTE_H
+
+#include <algorithm>
+#include <vector>
+
+#include <tiledb/tiledb>
+#include "soma_column.h"
+
+namespace tiledbsoma {
+using namespace tiledb;
+
+class SOMAAttribute : public SOMAColumn {
+   public:
+    /**
+     * Create a ``SOMAAttribute`` shared pointer from an Arrow schema
+     */
+    static std::shared_ptr<SOMAAttribute> create(
+        std::shared_ptr<Context> ctx,
+        ArrowSchema* schema,
+        std::string_view type_metadata,
+        PlatformConfig platform_config);
+
+    SOMAAttribute(
+        Attribute attribute,
+        std::optional<Enumeration> enumeration = std::nullopt)
+        : attribute(attribute)
+        , enumeration(enumeration) {
+    }
+
+    inline std::string name() const override {
+        return attribute.name();
+    }
+
+    inline bool isIndexColumn() const override {
+        return false;
+    }
+
+    inline void select_columns(
+        const std::unique_ptr<ManagedQuery>& query,
+        bool if_not_empty = false) const override {
+        query->select_columns(std::vector({attribute.name()}), if_not_empty);
+    };
+
+    inline soma_column_datatype_t type() const override {
+        return soma_column_datatype_t::SOMA_COLUMN_ATTRIBUTE;
+    }
+
+    inline std::optional<tiledb_datatype_t> domain_type() const override {
+        return std::nullopt;
+    }
+
+    inline std::optional<tiledb_datatype_t> data_type() const override {
+        return attribute.type();
+    }
+
+    inline std::optional<std::vector<Dimension>> tiledb_dimensions() override {
+        return std::nullopt;
+    }
+
+    inline std::optional<std::vector<Attribute>> tiledb_attributes() override {
+        return std::vector({attribute});
+    }
+
+    inline std::optional<std::vector<Enumeration>> tiledb_enumerations()
+        override {
+        if (!enumeration.has_value()) {
+            return std::nullopt;
+        }
+
+        return std::vector({enumeration.value()});
+    }
+
+    ArrowArray* arrow_domain_slot(
+        const SOMAContext& ctx,
+        Array& array,
+        enum Domainish kind) const override;
+
+    ArrowSchema* arrow_schema_slot(
+        const SOMAContext& ctx, Array& array) override;
+
+   private:
+    void _set_dim_points(
+        const std::unique_ptr<ManagedQuery>& query,
+        const SOMAContext& ctx,
+        const std::any& points) const override;
+
+    void _set_dim_ranges(
+        const std::unique_ptr<ManagedQuery>& query,
+        const SOMAContext& ctx,
+        const std::any& ranges) const override;
+
+    void _set_current_domain_slot(
+        NDRectangle& rectangle,
+        std::span<const std::any> domain) const override;
+
+    std::pair<bool, std::string> _can_set_current_domain_slot(
+        std::optional<NDRectangle>& rectangle,
+        std::span<const std::any> new_domain) const override;
+
+    std::any _core_domain_slot() const override;
+
+    std::any _non_empty_domain_slot(Array& array) const override;
+
+    std::any _core_current_domain_slot(
+        const SOMAContext& ctx, Array& array) const override;
+
+    std::any _core_current_domain_slot(NDRectangle& ndrect) const override;
+
+    Attribute attribute;
+    std::optional<Enumeration> enumeration;
+};
+}  // namespace tiledbsoma
+
+#endif
diff --git a/libtiledbsoma/src/tiledbsoma/tiledbsoma b/libtiledbsoma/src/tiledbsoma/tiledbsoma
@@ -50,6 +50,7 @@
 #include "soma/soma_array.h"
 #include "soma/soma_collection.h"
 #include "soma/soma_column.h"
+#include "soma/soma_attribute.h"
 #include "soma/soma_dimension.h"
 #include "soma/soma_dataframe.h"
 #include "soma/soma_group.h"

diff --git a/libtiledbsoma/test/unit_soma_column.cc b/libtiledbsoma/test/unit_soma_column.cc
@@ -314,6 +314,11 @@ TEST_CASE_METHOD(
                 std::make_shared<SOMADimension>(SOMADimension(dimension)));
         }
 
+        for (size_t i = 0; i < sdf->tiledb_schema()->attribute_num(); ++i) {
+            columns.push_back(std::make_shared<SOMAAttribute>(
+                SOMAAttribute(sdf->tiledb_schema()->attribute(i))));
+        }
+
         CurrentDomain current_domain = sdf->get_current_domain_for_test();
 
         REQUIRE(!current_domain.is_empty());