WIP reintro cfg option

single-cell-data · Feb 21, 2024 · 568d2e4 · 568d2e4
1 parent c7fb0d6
commit 568d2e4
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Showing 2 changed files with 88 additions and 1 deletion.
diff --git a/libtiledbsoma/src/soma/soma_array.cc b/libtiledbsoma/src/soma/soma_array.cc
@@ -59,14 +59,36 @@ void SOMAArray::create(
 std::unique_ptr<SOMAArray> SOMAArray::open(
     OpenMode mode,
     std::string_view uri,
-    std::shared_ptr<SOMAContext> ctx,
     std::string_view name,
+    std::map<std::string, std::string> platform_config,
     std::vector<std::string> column_names,
     std::string_view batch_size,
     ResultOrder result_order,
     std::optional<std::pair<uint64_t, uint64_t>> timestamp) {
     LOG_DEBUG(
         fmt::format("[SOMAArray] static method 'cfg' opening array '{}'", uri));
+    return std::make_unique<SOMAArray>(
+        mode,
+        uri,
+        std::make_shared<SOMAContext>(platform_config),
+        name,
+        column_names,
+        batch_size,
+        result_order,
+        timestamp);
+}
+
+std::unique_ptr<SOMAArray> SOMAArray::open(
+    OpenMode mode,
+    std::string_view uri,
+    std::shared_ptr<SOMAContext> ctx,
+    std::string_view name,
+    std::vector<std::string> column_names,
+    std::string_view batch_size,
+    ResultOrder result_order,
+    std::optional<std::pair<uint64_t, uint64_t>> timestamp) {
+    LOG_DEBUG(
+        fmt::format("[SOMAArray] static method 'ctx' opening array '{}'", uri));
     return std::make_unique<SOMAArray>(
         mode,
         uri,
@@ -82,6 +104,24 @@ std::unique_ptr<SOMAArray> SOMAArray::open(
 //= public non-static
 //===================================================================
 
+SOMAArray::SOMAArray(
+    OpenMode mode,
+    std::string_view uri,
+    std::string_view name,
+    std::map<std::string, std::string> platform_config,
+    std::vector<std::string> column_names,
+    std::string_view batch_size,
+    ResultOrder result_order,
+    std::optional<std::pair<uint64_t, uint64_t>> timestamp)
+    : uri_(util::rstrip_uri(uri))
+    , result_order_(result_order)
+    , timestamp_(timestamp) {
+    ctx_ = std::make_shared<SOMAContext>(platform_config);
+    validate(mode, name, timestamp);
+    reset(column_names, batch_size, result_order);
+    fill_metadata_cache();
+}
+
 SOMAArray::SOMAArray(
     OpenMode mode,
     std::string_view uri,

diff --git a/libtiledbsoma/src/soma/soma_array.h b/libtiledbsoma/src/soma/soma_array.h
@@ -69,6 +69,31 @@ class SOMAArray : public SOMAObject {
         ArraySchema schema,
         std::string soma_type);
 
+    /**
+     * @brief Open an array at the specified URI and return SOMAArray
+     * object.
+     *
+     * @param mode read or write
+     * @param uri URI of the array
+     * @param name Name of the array
+     * @param platform_config Config parameter dictionary
+     * @param column_names Columns to read
+     * @param batch_size Read batch size
+     * @param result_order Read result order: automatic (default), rowmajor,
+     * or colmajor
+     * @param timestamp Optional pair indicating timestamp start and end
+     * @return std::unique_ptr<SOMAArray> SOMAArray
+     */
+    static std::unique_ptr<SOMAArray> open(
+        OpenMode mode,
+        std::string_view uri,
+        std::string_view name = "unnamed",
+        std::map<std::string, std::string> platform_config = {},
+        std::vector<std::string> column_names = {},
+        std::string_view batch_size = "auto",
+        ResultOrder result_order = ResultOrder::automatic,
+        std::optional<std::pair<uint64_t, uint64_t>> timestamp = std::nullopt);
+
     /**
      * @brief Open an array at the specified URI and return SOMAArray
      * object.
@@ -97,6 +122,28 @@ class SOMAArray : public SOMAObject {
     //===================================================================
     //= public non-static
     //===================================================================
+
+    /**
+     * @brief Construct a new SOMAArray object
+     *
+     * @param mode read or write
+     * @param uri URI of the array
+     * @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
+     * @param timestamp Timestamp
+     */
+    SOMAArray(
+        OpenMode mode,
+        std::string_view uri,
+        std::string_view name,
+        std::map<std::string, std::string> platform_config,
+        std::vector<std::string> column_names,
+        std::string_view batch_size,
+        ResultOrder result_order,
+        std::optional<std::pair<uint64_t, uint64_t>> timestamp = std::nullopt);
 
     /**
      * @brief Construct a new SOMAArray object