Geometry dataframe implementation, use spatial axes when available wh…

…en creating schema

libtiledbsoma/src/CMakeLists.txt

@@ -37,6 +37,7 @@ add_library(TILEDB_SOMA_OBJECTS OBJECT
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_experiment.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_measurement.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_scene.cc
+  ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_geometry_dataframe.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_point_cloud_dataframe.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_multiscale_image.cc
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_context.cc
@@ -188,6 +189,7 @@ endif()
 #   ${CMAKE_CURRENT_SOURCE_DIR}/cpp_api/soma_experiment.h
 #   ${CMAKE_CURRENT_SOURCE_DIR}/cpp_api/soma_measurement.h
 #   ${CMAKE_CURRENT_SOURCE_DIR}/cpp_api/soma_scene.h
+#   ${CMAKE_CURRENT_SOURCE_DIR}/cpp_api/soma_geometry_dataframe.h
 #   ${CMAKE_CURRENT_SOURCE_DIR}/cpp_api/soma_point_cloud_dataframe.h
 #   ${CMAKE_CURRENT_SOURCE_DIR}/cpp_api/soma_multiscale_image.h
 #   ${CMAKE_CURRENT_SOURCE_DIR}/cpp_api/soma_object.h
@@ -211,6 +213,7 @@ install(FILES
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_experiment.h
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_measurement.h
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_scene.h
+  ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_geometry_dataframe.h
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_point_cloud_dataframe.h
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_multiscale_image.h
   ${CMAKE_CURRENT_SOURCE_DIR}/soma/soma_object.h

libtiledbsoma/src/soma/soma_geometry_dataframe.cc

@@ -0,0 +1,125 @@
+/**
+ * @file   soma_geometry_dataframe.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 SOMAGeometryDataFrame class.
+ */
+
+#include "soma_geometry_dataframe.h"
+#include "../utils/util.h"
+
+#include <regex>
+
+namespace tiledbsoma {
+using namespace tiledb;
+
+//===================================================================
+//= public static
+//===================================================================
+
+void SOMAGeometryDataFrame::create(
+    std::string_view uri,
+    std::unique_ptr<ArrowSchema> schema,
+    ArrowTable index_columns,
+    ArrowTable spatial_columns,
+    std::shared_ptr<SOMAContext> ctx,
+    PlatformConfig platform_config,
+    std::optional<TimestampRange> timestamp) {
+    std::vector<std::string> spatial_axes;
+    auto tiledb_schema = ArrowAdapter::tiledb_schema_from_arrow_schema(
+        ctx->tiledb_ctx(),
+        std::move(schema),
+        ArrowTable(
+            std::move(index_columns.first), std::move(index_columns.second)),
+        "SOMAGeometryDataFrame",
+        true,
+        platform_config,
+        ArrowTable(
+            std::move(spatial_columns.first),
+            std::move(spatial_columns.second)));
+    auto array = SOMAArray::create(
+        ctx, uri, tiledb_schema, "SOMAGeometryDataFrame", timestamp);
+}
+
+std::unique_ptr<SOMAGeometryDataFrame> SOMAGeometryDataFrame::open(
+    std::string_view uri,
+    OpenMode mode,
+    std::shared_ptr<SOMAContext> ctx,
+    std::vector<std::string> column_names,
+    ResultOrder result_order,
+    std::optional<TimestampRange> timestamp) {
+    return std::make_unique<SOMAGeometryDataFrame>(
+        mode, uri, ctx, column_names, result_order, timestamp);
+}
+
+bool SOMAGeometryDataFrame::exists(
+    std::string_view uri, std::shared_ptr<SOMAContext> ctx) {
+    try {
+        auto obj = SOMAObject::open(uri, OpenMode::read, ctx);
+        return "SOMAGeometryDataFrame" == obj->type();
+    } catch (TileDBSOMAError& e) {
+        return false;
+    }
+}
+
+//===================================================================
+//= public non-static
+//===================================================================
+
+std::unique_ptr<ArrowSchema> SOMAGeometryDataFrame::schema() const {
+    return this->arrow_schema();
+}
+
+const std::vector<std::string> SOMAGeometryDataFrame::index_column_names()
+    const {
+    return this->dimension_names();
+}
+
+const std::vector<std::string> SOMAGeometryDataFrame::spatial_column_names()
+    const {
+    std::vector<std::string> names;
+    std::unordered_set<std::string> unique_names;
+    std::regex rgx("tiledb__internal__(\\S+)__");
+    std::smatch matches;
+    for (auto dimension : this->dimension_names()) {
+        if (std::regex_search(dimension, matches, rgx)) {
+            if (unique_names.count(matches[1].str()) == 0) {
+                unique_names.insert(matches[1].str());
+                names.push_back(matches[1].str());
+            }
+        }
+    }
+
+    return names;
+}
+
+uint64_t SOMAGeometryDataFrame::count() {
+    return this->nnz();
+}
+
+}  // namespace tiledbsoma

libtiledbsoma/src/soma/soma_geometry_dataframe.h

@@ -0,0 +1,179 @@
+/**
+ * @file   soma_geometry_dataframe.h
+ *
+ * @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 SOMAGeometryDataFrame class.
+ */
+
+#ifndef SOMA_GEOMETRY_DATAFRAME
+#define SOMA_GEOMETRY_DATAFRAME
+
+#include <filesystem>
+
+#include "soma_array.h"
+
+namespace tiledbsoma {
+
+class ArrayBuffers;
+
+using namespace tiledb;
+
+class SOMAGeometryDataFrame : virtual public SOMAArray {
+   public:
+    //===================================================================
+    //= public static
+    //===================================================================
+
+    /**
+     * @brief Create a SOMAGeometryDataFrame object at the given URI.
+     *
+     * @param uri URI to create the SOMAGeometryDataFrame
+     * @param schema Arrow schema
+     * @param index_columns The index column names with associated domains
+     * and tile extents per dimension
+     * @param spatial_columns The spatial column names with associated domains
+     * and tile extents per dimension
+     * @param ctx SOMAContext
+     * @param platform_config Optional config parameter dictionary
+     * @param timestamp Optional the timestamp range to write SOMA metadata info
+     */
+    static void create(
+        std::string_view uri,
+        std::unique_ptr<ArrowSchema> schema,
+        ArrowTable index_columns,
+        ArrowTable spatial_columns,
+        std::shared_ptr<SOMAContext> ctx,
+        PlatformConfig platform_config = PlatformConfig(),
+        std::optional<TimestampRange> timestamp = std::nullopt);
+
+    /**
+     * @brief Open and return a SOMAGeometryDataFrame object at the given URI.
+     *
+     * @param uri URI to create the SOMAGeometryDataFrame
+     * @param mode read or write
+     * @param ctx SOMAContext
+     * @param column_names A list of column names to use as user-defined index
+     * columns (e.g., ``['cell_type', 'tissue_type']``). All named columns must
+     * exist in the schema, and at least one index column name is required.
+     * @param result_order Read result order: automatic (default), rowmajor, or
+     * colmajor
+     * @param timestamp If specified, overrides the default timestamp used to
+     * open this object. If unset, uses the timestamp provided by the context.
+     * @return std::unique_ptr<SOMAGeometryDataFrame> SOMAGeometryDataFrame
+     */
+    static std::unique_ptr<SOMAGeometryDataFrame> open(
+        std::string_view uri,
+        OpenMode mode,
+        std::shared_ptr<SOMAContext> ctx,
+        std::vector<std::string> column_names = {},
+        ResultOrder result_order = ResultOrder::automatic,
+        std::optional<TimestampRange> timestamp = std::nullopt);
+
+    /**
+     * @brief Check if the SOMAGeometryDataFrame exists at the URI.
+     *
+     * @param uri URI to create the SOMAGeometryDataFrame
+     * @param ctx SOMAContext
+     */
+    static bool exists(std::string_view uri, std::shared_ptr<SOMAContext> ctx);
+
+    //===================================================================
+    //= public non-static
+    //===================================================================
+
+    /**
+     * @brief Construct a new SOMAGeometryDataFrame object.
+     *
+     * @param mode read or write
+     * @param uri URI of the array
+     * @param ctx TileDB context
+     * @param column_names Columns to read
+     * @param result_order Read result order: automatic (default), rowmajor, or
+     * colmajor
+     * @param timestamp Timestamp
+     */
+    SOMAGeometryDataFrame(
+        OpenMode mode,
+        std::string_view uri,
+        std::shared_ptr<SOMAContext> ctx,
+        std::vector<std::string> column_names,
+        ResultOrder result_order,
+        std::optional<TimestampRange> timestamp = std::nullopt)
+        : SOMAArray(
+              mode,
+              uri,
+              ctx,
+              std::filesystem::path(uri).filename().string(),  // array name
+              column_names,
+              "auto",  // batch_size
+              result_order,
+              timestamp) {
+    }
+
+    SOMAGeometryDataFrame(const SOMAArray& other)
+        : SOMAArray(other) {
+    }
+
+    SOMAGeometryDataFrame() = delete;
+    SOMAGeometryDataFrame(const SOMAGeometryDataFrame&) = default;
+    SOMAGeometryDataFrame(SOMAGeometryDataFrame&&) = delete;
+    ~SOMAGeometryDataFrame() = default;
+
+    using SOMAArray::open;
+
+    /**
+     * Return the data schema, in the form of a ArrowSchema.
+     *
+     * @return std::unique_ptr<ArrowSchema>
+     */
+    std::unique_ptr<ArrowSchema> schema() const;
+
+    /**
+     * Return the index (dimension) column names.
+     *
+     * @return std::vector<std::string>
+     */
+    const std::vector<std::string> index_column_names() const;
+
+    /**
+     * Return the spatial column names.
+     *
+     * @return std::vector<std::string>
+     */
+    const std::vector<std::string> spatial_column_names() const;
+
+    /**
+     * Return the number of rows.
+     *
+     * @return int64_t
+     */
+    uint64_t count();
+};
+}  // namespace tiledbsoma
+
+#endif  // SOMA_GEOMETRY_DATAFRAME

libtiledbsoma/src/soma/soma_object.cc

@@ -7,6 +7,7 @@
 #include "soma_dataframe.h"
 #include "soma_dense_ndarray.h"
 #include "soma_experiment.h"
+#include "soma_geometry_dataframe.h"
 #include "soma_measurement.h"
 #include "soma_multiscale_image.h"
 #include "soma_point_cloud_dataframe.h"
@@ -61,8 +62,7 @@ std::unique_ptr<SOMAObject> SOMAObject::open(
         } else if (array_type == "somapointclouddataframe") {
             return std::make_unique<SOMAPointCloudDataFrame>(*array_);
         } else if (array_type == "somageometrydataframe") {
-            throw TileDBSOMAError(
-                "Support for SOMAGeometryDataFrame is not yet implemented");
+            return std::make_unique<SOMAGeometryDataFrame>(*array_);
         } else {
             throw TileDBSOMAError("Saw invalid SOMAArray type");
         }

libtiledbsoma/src/tiledbsoma/tiledbsoma

@@ -54,6 +54,7 @@
 #include "soma/soma_experiment.h"
 #include "soma/soma_measurement.h"
 #include "soma/soma_scene.h"
+#include "soma/soma_geometry_dataframe.h"
 #include "soma/soma_point_cloud_dataframe.h"
 #include "soma/soma_multiscale_image.h"
 #include "soma/soma_object.h"