Use DataProtocol exposed by core

Author: XanthosXanthopoulos

libtiledbvcf/src/dataset/tiledbvcfdataset.cc

@@ -317,13 +317,10 @@ void TileDBVCFDataset::create_empty_metadata(
     const std::string& root_uri,
     const Metadata& metadata,
     const tiledb_filter_type_t& checksum) {
-  utils::TileDBDataProtocol protocol =
-      utils::detect_tiledb_data_protocol(root_uri, ctx);
-
   create_group(ctx, metadata_group_uri(root_uri));
   create_sample_header_array(ctx, root_uri, checksum);
 
-  if (protocol == utils::TileDBDataProtocol::TILEDBV2) {
+  if (ctx.data_protocol(root_uri) == tiledb::Context::DataProtocol::v2) {
     // Group assets use full paths for tiledb cloud, relative paths otherwise
     bool relative = !cloud_dataset(root_uri);
 
@@ -364,9 +361,6 @@ void TileDBVCFDataset::create_empty_data_array(
     const bool allow_duplicates,
     const bool compress_sample_dim,
     const int compression_level) {
-  utils::TileDBDataProtocol protocol =
-      utils::detect_tiledb_data_protocol(root_uri, ctx);
-
   ArraySchema schema(ctx, TILEDB_SPARSE);
   schema.set_capacity(metadata.tile_capacity);
   schema.set_order({{TILEDB_ROW_MAJOR, TILEDB_ROW_MAJOR}});
@@ -475,7 +469,7 @@ void TileDBVCFDataset::create_empty_data_array(
 
   Array::create(data_array_uri(root_uri), schema);
 
-  if (protocol == utils::TileDBDataProtocol::TILEDBV2) {
+  if (ctx.data_protocol(root_uri) == tiledb::Context::DataProtocol::v2) {
     // Add the array to the root group
     // Group assests use full paths for tiledb cloud, relative paths otherwise
     bool relative = !cloud_dataset(root_uri);
@@ -1110,8 +1104,7 @@ std::unique_ptr<tiledb::Array> TileDBVCFDataset::open_vcf_array(
   // We are opening a legacy dataset where the `vcf_headers` array is
   // registered under the root group
   if (utils::has_member(*root_group, VCF_HEADER_ARRAY)) {
-    if (utils::detect_tiledb_data_protocol(root_uri_, *ctx_) ==
-        utils::TileDBDataProtocol::TILEDBV3) {
+    if (ctx_->data_protocol(root_uri_) == tiledb::Context::DataProtocol::v3) {
       // This is an legacy dataset registered under TileDB Carrara
       throw std::runtime_error(
           "Cannot open TileDB-VCF dataset; dataset '" + root_uri_ +

libtiledbvcf/src/stats/allele_count.cc

@@ -39,9 +39,6 @@ void AlleleCount::create(
     Context& ctx, const std::string& root_uri, tiledb_filter_type_t checksum) {
   LOG_DEBUG("[AlleleCount] Create array");
 
-  utils::TileDBDataProtocol protocol =
-      utils::detect_tiledb_data_protocol(root_uri, ctx);
-
   // Create filter lists
   FilterList rle_coord_filters(ctx);
   FilterList int_coord_filters(ctx);
@@ -109,7 +106,7 @@ void AlleleCount::create(
   Array array(ctx, uri, TILEDB_WRITE);
   array.put_metadata("version", TILEDB_UINT32, 1, &ALLELE_COUNT_VERSION);
 
-  if (protocol == utils::TileDBDataProtocol::TILEDBV2) {
+  if (ctx.data_protocol(root_uri) == tiledb::Context::DataProtocol::v2) {
     // Add array to root group
     // Group assets use full paths for tiledb cloud, relative paths otherwise
     auto relative = !utils::starts_with(root_uri, "tiledb://");

libtiledbvcf/src/stats/sample_stats.cc

@@ -49,9 +49,6 @@ SampleStats::~SampleStats() {
 
 void SampleStats::create(
     Context& ctx, const std::string& root_uri, int compression_level) {
-  utils::TileDBDataProtocol protocol =
-      utils::detect_tiledb_data_protocol(root_uri, ctx);
-
   // Create filter lists
   FilterList int_fl(ctx);
   FilterList float_fl(ctx);
@@ -143,7 +140,7 @@ void SampleStats::create(
   Array array(ctx, uri, TILEDB_WRITE);
   array.put_metadata("version", TILEDB_INT32, 1, &SAMPLE_STATS_VERSION);
 
-  if (protocol == utils::TileDBDataProtocol::TILEDBV2) {
+  if (ctx.data_protocol(root_uri) == tiledb::Context::DataProtocol::v2) {
     // Add array to root group
     // Group assets use full paths for tiledb cloud, relative paths otherwise
     auto relative = !utils::starts_with(root_uri, "tiledb://");

libtiledbvcf/src/stats/variant_stats.cc

@@ -57,9 +57,6 @@ void VariantStats::create(
     Context& ctx, const std::string& root_uri, tiledb_filter_type_t checksum) {
   LOG_DEBUG("[VariantStats] Create array");
 
-  utils::TileDBDataProtocol protocol =
-      utils::detect_tiledb_data_protocol(root_uri, ctx);
-
   // Create filter lists
   FilterList rle_coord_filters(ctx);
   FilterList int_coord_filters(ctx);
@@ -160,7 +157,7 @@ void VariantStats::create(
   Array array(ctx, uri, TILEDB_WRITE);
   array.put_metadata("version", TILEDB_UINT32, 1, &array_version_);
 
-  if (protocol == utils::TileDBDataProtocol::TILEDBV2) {
+  if (ctx.data_protocol(root_uri) == tiledb::Context::DataProtocol::v2) {
     // Add array to root group
     // Group assests use full paths for tiledb cloud, relative paths otherwise
     auto relative = !utils::starts_with(root_uri, "tiledb://");

libtiledbvcf/src/utils/uri.cc

@@ -91,29 +91,8 @@ std::string root_uri(
   return utils::uri_join(root, array);
 }
 
-TileDBDataProtocol detect_tiledb_data_protocol(
-    std::string_view uri, const Context& ctx) {
-  if (!uri.starts_with("tiledb")) {
-    return TileDBDataProtocol::TILEDBV2;
-  }
-
-  if (ctx.config().contains("rest.server_address")) {
-    auto rest_server = ctx.config().get("rest.server_address");
-
-    if (rest_server == "https://api.tiledb.com" ||
-        rest_server == "https://api.dev.tiledb.io") {
-      return TileDBDataProtocol::TILEDBV2;
-    }
-
-    return TileDBDataProtocol::TILEDBV3;
-  }
-
-  throw std::runtime_error(
-      "Unknown TileDB Data Protocol. Missing rest server address.");
-}
-
 void validate_uri(std::string_view uri, const Context& ctx) {
-  if (detect_tiledb_data_protocol(uri, ctx) == TileDBDataProtocol::TILEDBV2) {
+  if (ctx.data_protocol(uri.data()) == tiledb::Context::DataProtocol::v2) {
     return;
   }
 

libtiledbvcf/src/utils/uri.h

@@ -36,8 +36,6 @@ namespace vcf {
 
 namespace utils {
 
-enum class TileDBDataProtocol { TILEDBV2, TILEDBV3 };
-
 /** Ensure URI ends in / if a dir */
 void normalize_uri(std::string& uri, bool is_dir);
 
@@ -84,19 +82,6 @@ std::string group_uri(const Group& group, std::string_view array);
 std::string root_uri(
     std::string_view root_uri, std::string_view array, bool relative = false);
 
-/**
- * Detect the TileDB DataProtocol (legacy or TileDB 3.0+) based on the rest
- * server parameter in the TileDB config
- *
- * @param uri URI to to check
- * @param ctx TileDB context
- * @return The DataProtocol to be be used
- *
- * @remark This is a temprorary solution until a new API is available in 2.30
- */
-TileDBDataProtocol detect_tiledb_data_protocol(
-    std::string_view uri, const Context& ctx);
-
 /**
  * Checks whether or not the passed in URI contains illegal characters based on
  * the selected DataProtocol