[c++] Addition of ArrowSchema to TileDB ArraySchema Converter

libtiledbsoma/src/soma/soma_array.h

@@ -5,7 +5,7 @@
  *
  * The MIT License
  *
- * @copyright Copyright (c) 2022-2023 TileDB, Inc.
+ * @copyright Copyright (c) 2022-2024 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
@@ -102,8 +102,7 @@ class SOMAArray : public SOMAObject {
      *
      * @param mode read or write
      * @param uri URI of the array
-     * @param name Name of the array
-     * @param platform_config Config parameter dictionary
+     * @param ctx SOMAContext
      * @param column_names Columns to read
      * @param batch_size Read batch size
      * @param result_order Read result order: automatic (default), rowmajor,
@@ -152,8 +151,8 @@ class SOMAArray : public SOMAObject {
      *
      * @param mode read or write
      * @param uri URI of the array
+     * @param ctx SOMAContext
      * @param name name of the array
-     * @param platform_config Config parameter dictionary
      * @param column_names Columns to read
      * @param batch_size Batch size
      * @param result_order Result order

libtiledbsoma/src/soma/soma_collection.cc

@@ -41,12 +41,11 @@ using namespace tiledb;
 //= public static
 //===================================================================
 
-std::unique_ptr<SOMACollection> SOMACollection::create(
+void SOMACollection::create(
     std::string_view uri,
     std::shared_ptr<SOMAContext> ctx,
     std::optional<TimestampRange> timestamp) {
-    auto soma_group = SOMAGroup::create(ctx, uri, "SOMACollection", timestamp);
-    return std::make_unique<SOMACollection>(*soma_group);
+    SOMAGroup::create(ctx, uri, "SOMACollection", timestamp);
 }
 
 std::unique_ptr<SOMACollection> SOMACollection::open(
@@ -111,8 +110,11 @@ std::shared_ptr<SOMAExperiment> SOMACollection::add_new_experiment(
     std::string_view uri,
     URIType uri_type,
     std::shared_ptr<SOMAContext> ctx,
-    ArraySchema schema) {
-    SOMAExperiment::create(uri, schema, ctx);
+    std::unique_ptr<ArrowSchema> schema,
+    ColumnIndexInfo index_columns,
+    std::optional<PlatformConfig> platform_config) {
+    SOMAExperiment::create(
+        uri, std::move(schema), index_columns, ctx, platform_config);
     std::shared_ptr<SOMAExperiment> member = SOMAExperiment::open(
         uri, OpenMode::read, ctx);
     this->set(std::string(uri), uri_type, std::string(key));
@@ -125,8 +127,9 @@ std::shared_ptr<SOMAMeasurement> SOMACollection::add_new_measurement(
     std::string_view uri,
     URIType uri_type,
     std::shared_ptr<SOMAContext> ctx,
-    ArraySchema schema) {
-    SOMAMeasurement::create(uri, schema, ctx);
+    std::unique_ptr<ArrowSchema> schema,
+    ColumnIndexInfo index_columns) {
+    SOMAMeasurement::create(uri, std::move(schema), index_columns, ctx);
     std::shared_ptr<SOMAMeasurement> member = SOMAMeasurement::open(
         uri, OpenMode::read, ctx);
     this->set(std::string(uri), uri_type, std::string(key));
@@ -139,8 +142,11 @@ std::shared_ptr<SOMADataFrame> SOMACollection::add_new_dataframe(
     std::string_view uri,
     URIType uri_type,
     std::shared_ptr<SOMAContext> ctx,
-    ArraySchema schema) {
-    SOMADataFrame::create(uri, schema, ctx);
+    std::unique_ptr<ArrowSchema> schema,
+    ColumnIndexInfo index_columns,
+    std::optional<PlatformConfig> platform_config) {
+    SOMADataFrame::create(
+        uri, std::move(schema), index_columns, ctx, platform_config);
     std::shared_ptr<SOMADataFrame> member = SOMADataFrame::open(
         uri, OpenMode::read, ctx);
     this->set(std::string(uri), uri_type, std::string(key));
@@ -154,7 +160,7 @@ std::shared_ptr<SOMADenseNDArray> SOMACollection::add_new_dense_ndarray(
     URIType uri_type,
     std::shared_ptr<SOMAContext> ctx,
     ArraySchema schema) {
-    SOMADenseNDArray::create(uri, schema, ctx);
+    SOMADenseNDArray::create(uri, std::move(schema), ctx);
     std::shared_ptr<SOMADenseNDArray> member = SOMADenseNDArray::open(
         uri, OpenMode::read, ctx);
     this->set(std::string(uri), uri_type, std::string(key));
@@ -168,7 +174,7 @@ std::shared_ptr<SOMASparseNDArray> SOMACollection::add_new_sparse_ndarray(
     URIType uri_type,
     std::shared_ptr<SOMAContext> ctx,
     ArraySchema schema) {
-    SOMASparseNDArray::create(uri, schema, ctx);
+    SOMASparseNDArray::create(uri, std::move(schema), ctx);
     std::shared_ptr<SOMASparseNDArray> member = SOMASparseNDArray::open(
         uri, OpenMode::read, ctx);
     this->set(std::string(uri), uri_type, std::string(key));

libtiledbsoma/src/soma/soma_collection.h

@@ -61,7 +61,7 @@ class SOMACollection : public SOMAGroup {
      * @param ctx TileDB context
      * @param uri URI to create the SOMACollection
      */
-    static std::unique_ptr<SOMACollection> create(
+    static void create(
         std::string_view uri,
         std::shared_ptr<SOMAContext> ctx,
         std::optional<TimestampRange> timestamp = std::nullopt);
@@ -157,7 +157,9 @@ class SOMACollection : public SOMAGroup {
         std::string_view uri,
         URIType uri_type,
         std::shared_ptr<SOMAContext> ctx,
-        ArraySchema schema);
+        std::unique_ptr<ArrowSchema> schema,
+        ColumnIndexInfo index_columns,
+        std::optional<PlatformConfig> platform_config = std::nullopt);
 
     /**
      * Create and add a SOMAMeasurement to the SOMACollection.
@@ -172,7 +174,8 @@ class SOMACollection : public SOMAGroup {
         std::string_view uri,
         URIType uri_type,
         std::shared_ptr<SOMAContext> ctx,
-        ArraySchema schema);
+        std::unique_ptr<ArrowSchema> schema,
+        ColumnIndexInfo index_columns);
 
     /**
      * Create and add a SOMADataFrame to the SOMACollection.
@@ -187,7 +190,9 @@ class SOMACollection : public SOMAGroup {
         std::string_view uri,
         URIType uri_type,
         std::shared_ptr<SOMAContext> ctx,
-        ArraySchema schema);
+        std::unique_ptr<ArrowSchema> schema,
+        ColumnIndexInfo index_columns,
+        std::optional<PlatformConfig> platform_config = std::nullopt);
 
     /**
      * Create and add a SOMADenseNDArray to the SOMACollection.

libtiledbsoma/src/soma/soma_dataframe.cc

@@ -39,14 +39,16 @@ using namespace tiledb;
 //= public static
 //===================================================================
 
-std::unique_ptr<SOMADataFrame> SOMADataFrame::create(
+void SOMADataFrame::create(
     std::string_view uri,
-    ArraySchema schema,
+    std::unique_ptr<ArrowSchema> schema,
+    ColumnIndexInfo index_columns,
     std::shared_ptr<SOMAContext> ctx,
+    std::optional<PlatformConfig> platform_config,
     std::optional<TimestampRange> timestamp) {
-    auto soma_array = SOMAArray::create(
-        ctx, uri, schema, "SOMADataFrame", timestamp);
-    return std::make_unique<SOMADataFrame>(*soma_array);
+    auto tiledb_schema = ArrowAdapter::tiledb_schema_from_arrow_schema(
+        ctx->tiledb_ctx(), std::move(schema), index_columns, platform_config);
+    SOMAArray::create(ctx, uri, tiledb_schema, "SOMADataFrame", timestamp);
 }
 
 std::unique_ptr<SOMADataFrame> SOMADataFrame::open(

libtiledbsoma/src/soma/soma_dataframe.h

@@ -5,7 +5,7 @@
  *
  * The MIT License
  *
- * @copyright Copyright (c) 2023 TileDB, Inc.
+ * @copyright Copyright (c) 2023-2024 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
@@ -52,33 +52,36 @@ class SOMADataFrame : public SOMAArray {
     /**
      * @brief Create a SOMADataFrame object at the given URI.
      *
-     * @param uri URI to create the SOMAArray
-     * @param schema TileDB ArraySchema
+     * @param uri URI to create the SOMADataFrame
+     * @param schema Arrow schema
+     * @param index_columns The index column names with associated domains
+     * and tile extents per dimension
      * @param ctx SOMAContext
-     * @param timestamp Optional pair indicating timestamp start and end
-     * @return std::unique_ptr<SOMADataFrame>
+     * @param platform_config Optional config parameter dictionary
+     * @param timestamp Optional the timestamp range to write SOMA metadata info
      */
-    static std::unique_ptr<SOMADataFrame> create(
+    static void create(
         std::string_view uri,
-        ArraySchema schema,
+        std::unique_ptr<ArrowSchema> schema,
+        ColumnIndexInfo index_columns,
         std::shared_ptr<SOMAContext> ctx,
+        std::optional<PlatformConfig> platform_config = std::nullopt,
         std::optional<TimestampRange> timestamp = std::nullopt);
 
     /**
      * @brief Open and return a SOMADataFrame object at the given URI.
      *
-     * @param mode read or write
      * @param uri URI to create the SOMADataFrame
+     * @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 platform_config Platform-specific options used to create this
-     * DataFrame
      * @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<SOMADataFrame>
+     * @return std::unique_ptr<SOMADataFrame> SOMADataFrame
      */
     static std::unique_ptr<SOMADataFrame> open(
         std::string_view uri,

libtiledbsoma/src/soma/soma_dense_ndarray.cc

@@ -29,7 +29,6 @@
  *
  *   This file defines the SOMADenseNDArray class.
  */
-
 #include "soma_dense_ndarray.h"
 
 namespace tiledbsoma {
@@ -39,14 +38,12 @@ using namespace tiledb;
 //= public static
 //===================================================================
 
-std::unique_ptr<SOMADenseNDArray> SOMADenseNDArray::create(
+void SOMADenseNDArray::create(
     std::string_view uri,
     ArraySchema schema,
     std::shared_ptr<SOMAContext> ctx,
     std::optional<TimestampRange> timestamp) {
-    auto soma_array = SOMAArray::create(
-        ctx, uri, schema, "SOMADenseNDArray", timestamp);
-    return std::make_unique<SOMADenseNDArray>(*soma_array);
+    SOMAArray::create(ctx, uri, schema, "SOMADenseNDArray", timestamp);
 }
 
 std::unique_ptr<SOMADenseNDArray> SOMADenseNDArray::open(

libtiledbsoma/src/soma/soma_dense_ndarray.h

@@ -5,7 +5,7 @@
  *
  * The MIT License
  *
- * @copyright Copyright (c) 2023 TileDB, Inc.
+ * @copyright Copyright (c) 2023-2024 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
@@ -52,13 +52,12 @@ class SOMADenseNDArray : public SOMAArray {
     /**
      * @brief Create a SOMADenseNDArray object at the given URI.
      *
-     * @param uri URI to create the SOMAArray
-     * @param schema TileDB ArraySchema
+     * @param uri URI to create the SOMADenseNDArray
+     * @param schema Arrow schema
      * @param ctx SOMAContext
-     * @param timestamp Optional pair indicating timestamp start and end
-     * @return std::unique_ptr<SOMADenseNDArray>
+     * @param timestamp Optional the timestamp range to write SOMA metadata info
      */
-    static std::unique_ptr<SOMADenseNDArray> create(
+    static void create(
         std::string_view uri,
         ArraySchema schema,
         std::shared_ptr<SOMAContext> ctx,
@@ -67,18 +66,17 @@ class SOMADenseNDArray : public SOMAArray {
     /**
      * @brief Open and return a SOMADenseNDArray object at the given URI.
      *
-     * @param mode read or write
      * @param uri URI to create the SOMADenseNDArray
+     * @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 platform_config Platform-specific options used to create this
-     * SOMADenseNDArray
-     * @param timestamp If specified, overrides the default timestamp used to
-     * open this object. If unset, uses the timestamp provided by the context.
      * @param result_order Read result order: automatic (default), rowmajor, or
      * colmajor
-     * @return std::shared_ptr<SOMADenseNDArray>
+     * @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<SOMADenseNDArray> SOMADenseNDArray
      */
     static std::unique_ptr<SOMADenseNDArray> open(
         std::string_view uri,
@@ -105,6 +103,7 @@ class SOMADenseNDArray : public SOMAArray {
      * @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

libtiledbsoma/src/soma/soma_experiment.cc

@@ -41,19 +41,31 @@ using namespace tiledb;
 //= public static
 //===================================================================
 
-std::unique_ptr<SOMAExperiment> SOMAExperiment::create(
+void SOMAExperiment::create(
     std::string_view uri,
-    ArraySchema schema,
+    std::unique_ptr<ArrowSchema> schema,
+    ColumnIndexInfo index_columns,
     std::shared_ptr<SOMAContext> ctx,
+    std::optional<PlatformConfig> platform_config,
     std::optional<TimestampRange> timestamp) {
     std::string exp_uri(uri);
 
-    auto soma_group = SOMAGroup::create(ctx, uri, "SOMAExperiment", timestamp);
-    SOMADataFrame::create(exp_uri + "/obs", schema, ctx, timestamp);
+    SOMAGroup::create(ctx, exp_uri, "SOMAExperiment", timestamp);
+    SOMADataFrame::create(
+        exp_uri + "/obs",
+        std::move(schema),
+        index_columns,
+        ctx,
+        platform_config,
+        timestamp);
     SOMACollection::create(exp_uri + "/ms", ctx, timestamp);
-    soma_group->set(exp_uri + "/obs", URIType::absolute, "obs");
-    soma_group->set(exp_uri + "/ms", URIType::absolute, "ms");
-    return std::make_unique<SOMAExperiment>(*soma_group);
+
+    auto name = std::string(std::filesystem::path(uri).filename());
+    auto group = SOMAGroup::open(
+        OpenMode::write, exp_uri, ctx, name, timestamp);
+    group->set(exp_uri + "/obs", URIType::absolute, "obs");
+    group->set(exp_uri + "/ms", URIType::absolute, "ms");
+    group->close();
 }
 
 std::unique_ptr<SOMAExperiment> SOMAExperiment::open(

libtiledbsoma/src/soma/soma_experiment.h

@@ -54,10 +54,12 @@ class SOMAExperiment : public SOMACollection {
      * @param schema TileDB ArraySchema
      * @param platform_config Optional config parameter dictionary
      */
-    static std::unique_ptr<SOMAExperiment> create(
+    static void create(
         std::string_view uri,
-        ArraySchema schema,
+        std::unique_ptr<ArrowSchema> schema,
+        ColumnIndexInfo index_columns,
         std::shared_ptr<SOMAContext> ctx,
+        std::optional<PlatformConfig> platform_config = std::nullopt,
         std::optional<TimestampRange> timestamp = std::nullopt);
 
     /**