Merge pull request #23 from davidbrochart/local_fs

Overload hierarchy creation with local file system store

Author: JohanMabille

examples/explore_hierarchy.ipynb

@@ -146,8 +146,7 @@
    "outputs": [],
    "source": [
     ">xcpp14\n",
-    "xt::xzarr_file_system_store s1(\"test.zr3\");\n",
-    "auto h1 = xt::get_zarr_hierarchy(s1);"
+    "auto h1 = xt::get_zarr_hierarchy(\"test.zr3\");"
    ]
   },
   {

examples/zarr_v2.ipynb

@@ -191,8 +191,7 @@
    "source": [
     ">xcpp14\n",
     "xt::xzarr_register_compressor<xt::xzarr_file_system_store, xt::xio_blosc_config>();\n",
-    "xt::xzarr_file_system_store s(\"marie_curie.zarr\");\n",
-    "auto h = xt::get_zarr_hierarchy(s, \"2\");\n",
+    "auto h = xt::get_zarr_hierarchy(\"marie_curie.zarr\", \"2\");\n",
     "auto z = h.get_array(\"\");"
    ]
   },

examples/zarr_v3.ipynb

@@ -150,8 +150,7 @@
    "outputs": [],
    "source": [
     ">xcpp14\n",
-    "xt::xzarr_file_system_store s1(\"h_zarrita.zr3\");\n",
-    "auto h1 = xt::get_zarr_hierarchy(s1);\n",
+    "auto h1 = xt::get_zarr_hierarchy(\"h_zarrita.zr3\");\n",
     "xt::zarray z1 = h1.get_array(\"/arthur/dent\");"
    ]
   },
@@ -170,7 +169,7 @@
    "source": [
     ">xcpp14\n",
     "auto a1 = z1.get_array<double>();\n",
-    "std::cout << a1 << std::endl;"
+    "a1"
    ]
   },
   {
@@ -192,8 +191,7 @@
     "nlohmann::json attrs = {{\"question\", \"life\"}, {\"answer\", 42}};\n",
     "std::size_t pool_size = 1;\n",
     "double fill_value = 6.6;\n",
-    "xt::xzarr_file_system_store s2(\"h_xtensor.zr3\");\n",
-    "auto h2 = xt::create_zarr_hierarchy(s2);\n",
+    "auto h2 = xt::create_zarr_hierarchy(\"h_xtensor.zr3\");\n",
     "xt::zarray z2 = h2.create_array(\"/arthur/dent\", shape, chunk_shape, \"<f8\", 'C', '/', xt::xio_binary_config(), attrs, pool_size, fill_value);"
    ]
   },
@@ -262,7 +260,7 @@
     "auto h3 = xt::get_zarr_hierarchy(s3);\n",
     "xt::zarray z3 = h3.get_array(\"/arthur/dent\");\n",
     "auto a3 = z3.get_array<int32_t>();\n",
-    "std::cout << a3 << std::endl;"
+    "a3"
    ]
   }
  ],

include/xtensor-zarr/xzarr_hierarchy.hpp

@@ -16,6 +16,7 @@
 #include "xzarr_array.hpp"
 #include "xzarr_group.hpp"
 #include "xzarr_common.hpp"
+#include "xzarr_file_system_store.hpp"
 
 namespace xt
 {
@@ -50,7 +51,7 @@ namespace xt
         nlohmann::json get_nodes(const std::string& path="/");
 
     private:
-        store_type& m_store;
+        store_type m_store;
         std::string m_zarr_version;
     };
 
@@ -140,6 +141,17 @@ namespace xt
         return h;
     }
 
+    xzarr_hierarchy<xzarr_file_system_store> create_zarr_hierarchy(const char* local_store_path, const std::string& zarr_version = "3")
+    {
+        xzarr_file_system_store store(local_store_path);
+        return create_zarr_hierarchy(store, zarr_version);
+    }
+
+    xzarr_hierarchy<xzarr_file_system_store> create_zarr_hierarchy(const std::string& local_store_path, const std::string& zarr_version = "3")
+    {
+        return create_zarr_hierarchy(local_store_path.c_str(), zarr_version);
+    }
+
     /**
      * Accesses a Zarr hierarchy.
      * This function returns a ``xzarr_hierarchy`` handler to a hierarchy in a given store.
@@ -176,6 +188,18 @@ namespace xt
         xzarr_hierarchy<store_type> h(store, zarr_ver);
         return h;
     }
+
+    xzarr_hierarchy<xzarr_file_system_store> get_zarr_hierarchy(const char* local_store_path, const std::string& zarr_version = "0")
+    {
+        xzarr_file_system_store store(local_store_path);
+        return get_zarr_hierarchy(store, zarr_version);
+    }
+
+    xzarr_hierarchy<xzarr_file_system_store> get_zarr_hierarchy(const std::string& local_store_path, const std::string& zarr_version = "0")
+    {
+        return get_zarr_hierarchy(local_store_path.c_str(), zarr_version);
+    }
+
 }
 
 #endif

test/test_zarr.cpp

@@ -26,8 +26,7 @@ namespace xt
     TEST(xzarr_hierarchy, read_v2)
     {
         xzarr_register_compressor<xzarr_file_system_store, xio_gzip_config>();
-        xzarr_file_system_store s("h_zarr.zr2");
-        auto h = get_zarr_hierarchy(s);
+        auto h = get_zarr_hierarchy("h_zarr.zr2");
         zarray z = h.get_array("/arthur/dent");
         auto ref = arange(2 * 5).reshape({2, 5});
         auto a = z.get_array<double>();
@@ -37,8 +36,7 @@ namespace xt
 
     TEST(xzarr_hierarchy, read_array)
     {
-        xzarr_file_system_store s("h_zarrita.zr3");
-        auto h = get_zarr_hierarchy(s);
+        auto h = get_zarr_hierarchy("h_zarrita.zr3");
         zarray z = h.get_array("/arthur/dent");
         auto ref = arange(2 * 5).reshape({2, 5});
         auto a = z.get_array<double>();
@@ -53,8 +51,7 @@ namespace xt
         nlohmann::json attrs = {{"question", "life"}, {"answer", 42}};
         std::size_t pool_size = 1;
         double fill_value = 6.6;
-        xzarr_file_system_store s("h_xtensor.zr3");
-        auto h = create_zarr_hierarchy(s);
+        auto h = create_zarr_hierarchy("h_xtensor.zr3");
         zarray z1 = h.create_array("/arthur/dent", shape, chunk_shape, "<f8", 'C', '/', xio_gzip_config(), attrs, pool_size, fill_value);
         //xchunked_array_factory<xzarr_file_system_store>::add_dtype<half_float::half>("f2");
         //auto a1 = z1.get_array<double>();
@@ -80,8 +77,7 @@ namespace xt
 
     TEST(xzarr_hierarchy, create_group)
     {
-        xzarr_file_system_store store1("h_xtensor.zr3");
-        auto h1 = get_zarr_hierarchy(store1);
+        auto h1 = get_zarr_hierarchy("h_xtensor.zr3");
         nlohmann::json attrs = {{"heart", "gold"}, {"improbability", "infinite"}};
         auto g1 = h1.create_group("/tricia/mcmillan", attrs);
         // since "/tricia/mcmillan" is a group, it should not be possible to get it as an array
@@ -90,8 +86,7 @@ namespace xt
 
     TEST(xzarr_hierarchy, create_node)
     {
-        xzarr_file_system_store store1("h_xtensor.zr3");
-        auto h1 = get_zarr_hierarchy(store1);
+        auto h1 = get_zarr_hierarchy("h_xtensor.zr3");
         h1.create_group("/marvin");
         h1["/marvin"].create_group("paranoid");
         std::vector<size_t> shape = {5, 5};
@@ -103,8 +98,7 @@ namespace xt
 
     TEST(xzarr_hierarchy, explore)
     {
-        xzarr_file_system_store store1("h_xtensor.zr3");
-        auto h1 = get_zarr_hierarchy(store1);
+        auto h1 = get_zarr_hierarchy("h_xtensor.zr3");
         std::string children = h1.get_children("/").dump();
         std::string ref1 = "{\"arthur\":\"implicit_group\",\"marvin\":\"explicit_group\",\"tricia\":\"implicit_group\"}";
         EXPECT_EQ(children, ref1);
@@ -187,8 +181,7 @@ namespace xt
         std::size_t pool_size = 1;
         double fill_value = 6.6;
         std::string zarr_version = "2";
-        xzarr_file_system_store s("h_xtensor.zr2");
-        auto h = create_zarr_hierarchy(s, zarr_version);
+        auto h = create_zarr_hierarchy("h_xtensor.zr2", zarr_version);
         zarray z1 = h.create_array("/arthur/dent", shape, chunk_shape, "<f8", 'C', '.', xio_gzip_config(), attrs, pool_size, fill_value);
     }
 }