[c++] SOMAColumn part 1

apis/python/setup.py

@@ -253,7 +253,7 @@ def run(self):
     CXX_FLAGS.append(f'-Wl,-rpath,{str(tiledb_dir / "lib")}')
 
 if sys.platform == "darwin":
-    CXX_FLAGS.append("-mmacosx-version-min=11.0")
+    CXX_FLAGS.append("-mmacosx-version-min=13.3")
 
 if os.name == "posix" and sys.platform != "darwin":
     LIB_DIRS.append(str(tiledbsoma_dir / "lib" / "x86_64-linux-gnu"))

libtiledbsoma/src/CMakeLists.txt

@@ -33,6 +33,10 @@ add_library(TILEDB_SOMA_OBJECTS OBJECT
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_array.cc
   ${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_geometry_column.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_collection.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_experiment.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_measurement.cc
@@ -206,6 +210,10 @@ install(FILES
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/column_buffer.h
   ${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_geometry_column.h
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_collection.h
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_dataframe.h
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_dense_ndarray.h

libtiledbsoma/src/soma/enums.h

@@ -43,4 +43,18 @@ enum class ResultOrder { automatic = 0, rowmajor, colmajor };
 /** Defines whether the SOMAGroup URI is absolute or relative */
 enum class URIType { automatic = 0, absolute, relative };
 
+typedef enum {
+    SOMA_COLUMN_DIMENSION = 0,
+    SOMA_COLUMN_ATTRIBUTE = 1,
+    SOMA_COLUMN_GEOMETRY = 2
+} soma_column_datatype_t;
+
+// This enables some code deduplication between core domain, core current
+// domain, and core non-empty domain.
+enum class Domainish {
+    kind_core_domain = 0,
+    kind_core_current_domain = 1,
+    kind_non_empty_domain = 2
+};
+
 #endif  // SOMA_ENUMS

libtiledbsoma/src/soma/soma_array.h

@@ -90,14 +90,6 @@ using namespace tiledb;
 
 using StatusAndReason = std::pair<bool, std::string>;
 
-// This enables some code deduplication between core domain, core current
-// domain, and core non-empty domain.
-enum class Domainish {
-    kind_core_domain = 0,
-    kind_core_current_domain = 1,
-    kind_non_empty_domain = 2
-};
-
 class SOMAArray : public SOMAObject {
    public:
     friend class ManagedQuery;

libtiledbsoma/src/soma/soma_attribute.cc

@@ -0,0 +1,95 @@
+#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

libtiledbsoma/src/soma/soma_attribute.h

@@ -0,0 +1,119 @@
+#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 virtual 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) {
+    }
+
+    virtual inline std::string name() const override {
+        return attribute.name();
+    }
+
+    virtual inline bool isIndexColumn() const override {
+        return false;
+    }
+
+    virtual 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);
+    };
+
+    virtual inline soma_column_datatype_t type() const override {
+        return soma_column_datatype_t::SOMA_COLUMN_ATTRIBUTE;
+    }
+
+    virtual inline std::optional<tiledb_datatype_t> domain_type()
+        const override {
+        return std::nullopt;
+    }
+
+    virtual inline std::optional<tiledb_datatype_t> data_type() const override {
+        return attribute.type();
+    }
+
+    virtual inline std::optional<std::vector<Dimension>> tiledb_dimensions()
+        override {
+        return std::nullopt;
+    }
+
+    virtual inline std::optional<std::vector<Attribute>> tiledb_attributes()
+        override {
+        return std::vector({attribute});
+    }
+
+    virtual inline std::optional<std::vector<Enumeration>> tiledb_enumerations()
+        override {
+        if (!enumeration.has_value()) {
+            return std::nullopt;
+        }
+
+        return std::vector({enumeration.value()});
+    }
+
+    virtual ArrowArray* arrow_domain_slot(
+        const SOMAContext& ctx,
+        Array& array,
+        enum Domainish kind) const override;
+
+    virtual ArrowSchema* arrow_schema_slot(
+        const SOMAContext& ctx, Array& array) override;
+
+   private:
+    virtual void _set_dim_points(
+        const std::unique_ptr<ManagedQuery>& query,
+        const SOMAContext& ctx,
+        const std::any& points) const override;
+
+    virtual void _set_dim_ranges(
+        const std::unique_ptr<ManagedQuery>& query,
+        const SOMAContext& ctx,
+        const std::any& ranges) const override;
+
+    virtual void _set_current_domain_slot(
+        NDRectangle& rectangle,
+        std::span<const std::any> domain) const override;
+
+    virtual std::pair<bool, std::string> _can_set_current_domain_slot(
+        std::optional<NDRectangle>& rectangle,
+        std::span<const std::any> new_domain) const override;
+
+    virtual std::any _core_domain_slot() const override;
+
+    virtual std::any _non_empty_domain_slot(Array& array) const override;
+
+    virtual std::any _core_current_domain_slot(
+        const SOMAContext& ctx, Array& array) const override;
+
+    virtual std::any _core_current_domain_slot(
+        NDRectangle& ndrect) const override;
+
+    Attribute attribute;
+    std::optional<Enumeration> enumeration;
+};
+}  // namespace tiledbsoma
+
+#endif

libtiledbsoma/src/soma/soma_column.cc

@@ -0,0 +1,62 @@
+/**
+ * @file   soma_column.cc
+ *
+ * @section LICENSE
+ *
+ * The MIT License
+ *
+ * @copyright Copyright (c) 2024 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 SOMAColumn class.
+ */
+
+#include "soma_column.h"
+
+namespace tiledbsoma {
+
+template <>
+std::pair<std::string, std::string> SOMAColumn::core_domain_slot<std::string>()
+    const {
+    return std::pair<std::string, std::string>("", "");
+}
+
+template <>
+std::pair<std::string, std::string>
+SOMAColumn::core_current_domain_slot<std::string>(
+    const SOMAContext& ctx, Array& array) const {
+    try {
+        std::pair<std::string, std::string>
+            current_domain = std::any_cast<std::pair<std::string, std::string>>(
+                _core_current_domain_slot(ctx, array));
+
+        if (current_domain.first == "" && (current_domain.second == "\x7f" ||
+                                           current_domain.second == "\xff")) {
+            return std::pair<std::string, std::string>("", "");
+        }
+
+        return current_domain;
+    } catch (const std::exception& e) {
+        throw TileDBSOMAError(e.what());
+    }
+}
+}  // namespace tiledbsoma