[c++] Add helper methods to convert to ArrowSchema (#3424)

* Add helper methods for to and from arrow contructs * Remove unnecessary `std::string` conversion to `c_str` Co-authored-by: John Kerl <[email protected]> * lint fix * Switch C-style casts to named casts * [c++] Column abstraction: `SOMADimension`, part 1 (#3425) `SOMAColumn` provides an abstraction over TileDB attributes and dimensions and exposes a common interface for all columns regardless of type. Subclasses of `SOMAColumn` can implement complex indexing mechanism through additional dimensions and encapsulate all that logic in one place and make it modular. --------- Co-authored-by: John Kerl <[email protected]>
single-cell-data · Jan 2, 2025 · 9e7a461 · 9e7a461
1 parent fbeee6f
commit 9e7a461
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Showing 15 changed files with 2,237 additions and 29 deletions.
diff --git a/apis/python/setup.py b/apis/python/setup.py
@@ -254,7 +254,7 @@ 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"))

diff --git a/libtiledbsoma/src/CMakeLists.txt b/libtiledbsoma/src/CMakeLists.txt
@@ -33,6 +33,8 @@ 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_dimension.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 +208,8 @@ 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_dimension.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

diff --git a/libtiledbsoma/src/soma/enums.h b/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
diff --git a/libtiledbsoma/src/soma/soma_array.h b/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;

diff --git a/libtiledbsoma/src/soma/soma_column.cc b/libtiledbsoma/src/soma/soma_column.cc
@@ -0,0 +1,81 @@
+/**
+ * @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 {
+    // Here is an intersection of a few oddities:
+    //
+    // * Core domain for string dims must be a nullptr pair; it cannot
+    // be
+    //   anything else.
+    // * TileDB-Py shows this by using an empty-string pair, which we
+    //   imitate.
+    // * Core current domain for string dims must _not_ be a nullptr
+    // pair.
+    // * In TileDB-SOMA, unless the user specifies otherwise, we use ""
+    // for
+    //   min and "\x7f" for max. (We could use "\x7f" but that causes
+    //   display problems in Python.)
+    //
+    // To work with all these factors, if the current domain is the
+    // default
+    // "" to "\x7f", return an empty-string pair just as we do for
+    // domain. (There was some pre-1.15 software using "\xff" and it's
+    // super-cheap to check for that as well.)
+    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