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[c++] Addition of ArrowSchema to TileDB ArraySchema Converter (#2418
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* Use unique_ptr<ArrowSchema>
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@nguyenv
nguyenv authored Apr 17, 2024
1 parent 4f6b9ae commit 8c07c6f
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Showing 29 changed files with 676 additions and 288 deletions.
7 changes: 3 additions & 4 deletions libtiledbsoma/src/soma/soma_array.h
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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
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28 changes: 17 additions & 11 deletions libtiledbsoma/src/soma/soma_collection.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand Down Expand Up @@ -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));
Expand All @@ -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));
Expand All @@ -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));
Expand All @@ -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));
Expand All @@ -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));
Expand Down
13 changes: 9 additions & 4 deletions libtiledbsoma/src/soma/soma_collection.h
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
Expand Down Expand Up @@ -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.
Expand All @@ -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.
Expand All @@ -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.
Expand Down
12 changes: 7 additions & 5 deletions libtiledbsoma/src/soma/soma_dataframe.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand Down
25 changes: 14 additions & 11 deletions libtiledbsoma/src/soma/soma_dataframe.h
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down
7 changes: 2 additions & 5 deletions libtiledbsoma/src/soma/soma_dense_ndarray.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,6 @@
*
* This file defines the SOMADenseNDArray class.
*/

#include "soma_dense_ndarray.h"

namespace tiledbsoma {
Expand All @@ -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(
Expand Down
23 changes: 11 additions & 12 deletions libtiledbsoma/src/soma/soma_dense_ndarray.h
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand All @@ -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,
Expand All @@ -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
Expand Down
26 changes: 19 additions & 7 deletions libtiledbsoma/src/soma/soma_experiment.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand Down
6 changes: 4 additions & 2 deletions libtiledbsoma/src/soma/soma_experiment.h
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Original file line number Diff line number Diff line change
Expand Up @@ -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);

/**
Expand Down
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