Read in config

single-cell-data · Mar 25, 2024 · 0b029d7 · 0b029d7
1 parent 14e4846
commit 0b029d7
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Showing 4 changed files with 17 additions and 10 deletions.
diff --git a/apis/python/src/tiledbsoma/_dataframe.py b/apis/python/src/tiledbsoma/_dataframe.py
@@ -244,8 +244,8 @@ def create(
         domains = pa.StructArray.from_arrays(domains, names=index_column_names)
         extents = pa.StructArray.from_arrays(extents, names=index_column_names)
 
-        print(index_column_names)
-
+        print(platform_config)
+        
         # TODO add as kw args
         clib.SOMADataFrame.create(
             uri,
@@ -398,11 +398,6 @@ def read(
 
         if value_filter is not None:
             sr.set_condition(QueryCondition(value_filter), handle.schema)
-
-        print("sr.schema:")
-        print(sr.schema)
-        print("coords:")
-        print(coords)
 
         self._set_reader_coords(sr, coords)
 

diff --git a/libtiledbsoma/src/soma/soma_dataframe.cc b/libtiledbsoma/src/soma/soma_dataframe.cc
@@ -45,8 +45,10 @@ void SOMADataFrame::create(
     ColumnIndexInfo index_columns,
     std::shared_ptr<SOMAContext> ctx,
     std::optional<std::pair<uint64_t, uint64_t>> timestamp) {
+    PlatformConfig platform_cfg = {
+        {"tiledb", {{"create", {{"allow_duplicates", false}}}}}};
     auto tiledb_schema = ArrowAdapter::tiledb_schema_from_arrow_schema(
-        ctx->tiledb_ctx(), schema, index_columns);
+        ctx->tiledb_ctx(), schema, index_columns, platform_cfg);
     SOMAArray::create(ctx, uri, tiledb_schema, "SOMADataFrame", timestamp);
 }
 

diff --git a/libtiledbsoma/src/utils/arrow_adapter.cc b/libtiledbsoma/src/utils/arrow_adapter.cc
@@ -244,9 +244,15 @@ std::pair<const void*, std::size_t> ArrowAdapter::_get_data_and_length(
 ArraySchema ArrowAdapter::tiledb_schema_from_arrow_schema(
     std::shared_ptr<Context> ctx,
     std::shared_ptr<ArrowSchema> arrow_schema,
-    ColumnIndexInfo index_column_info) {
+    ColumnIndexInfo index_column_info,
+    PlatformConfig platform_config) {
     auto [index_column_names, domains, extents] = index_column_info;
 
+    std::cout << (platform_config["tiledb"]["create"]["allows_duplicates"] ?
+                      "yes" :
+                      "No")
+              << std::endl;
+
     ArraySchema schema(*ctx, TILEDB_SPARSE);
     Domain domain(*ctx);
 

diff --git a/libtiledbsoma/src/utils/arrow_adapter.h b/libtiledbsoma/src/utils/arrow_adapter.h
@@ -41,6 +41,9 @@ using ColumnIndexInfo = std::tuple<
     std::shared_ptr<ArrowArray>   // tile extent
     >;
 
+using PlatformConfig =
+    std::map<std::string, std::map<std::string, std::map<std::string, bool>>>;
+
 class ArrowAdapter {
    public:
     static void release_schema(struct ArrowSchema* schema);
@@ -70,7 +73,8 @@ class ArrowAdapter {
     static ArraySchema tiledb_schema_from_arrow_schema(
         std::shared_ptr<Context> ctx,
         std::shared_ptr<ArrowSchema> arrow_schema,
-        ColumnIndexInfo index_column_info);
+        ColumnIndexInfo index_column_info,
+        PlatformConfig platform_config);
 
     /**
      * @brief Get Arrow format string from TileDB datatype.