Merge pull request #35 from davidbrochart/group_v2

Support v2's groups
xtensor-stack · Mar 2, 2021 · dd9be1b · dd9be1b
2 parents 4e11824 + 6850ae3
commit dd9be1b
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Showing 4 changed files with 45 additions and 23 deletions.
diff --git a/include/xtensor-zarr/xzarr_array.hpp b/include/xtensor-zarr/xzarr_array.hpp
@@ -19,7 +19,7 @@
 namespace xt
 {
     template <class store_type, class shape_type, class C>
-    zarray create_zarr_array(store_type store, const std::string& path, shape_type shape, shape_type chunk_shape, const std::string& dtype, char chunk_memory_layout, char chunk_separator, const C& compressor, const nlohmann::json& attrs, std::size_t chunk_pool_size, const nlohmann::json& fill_value, const std::size_t zarr_version_major = 3)
+    zarray create_zarr_array(store_type store, const std::string& path, shape_type shape, shape_type chunk_shape, const std::string& dtype, char chunk_memory_layout, char chunk_separator, const C& compressor, const nlohmann::json& attrs, std::size_t chunk_pool_size, const nlohmann::json& fill_value, const std::size_t zarr_version_major)
     {
         nlohmann::json j;
         nlohmann::json compressor_config;
@@ -45,7 +45,11 @@ namespace xt
                 chunk_separator = '.';
                 j["dtype"] = dtype;
                 j["order"] = std::string(1, chunk_memory_layout);
-                if (compressor.name != "binary")
+                if (compressor.name == "binary")
+                {
+                    j["compressor"] = nlohmann::json();
+                }
+                else
                 {
                     compressor.write_to(compressor_config);
                     j["compressor"] = compressor_config;
@@ -77,11 +81,11 @@ namespace xt
             default:
                 break;
         }
-        return xchunked_array_factory<store_type>::build(store, compressor.name, dtype, chunk_memory_layout, shape, chunk_shape, full_path, chunk_separator, attrs, compressor_config, chunk_pool_size, fill_value, 3);
+        return xchunked_array_factory<store_type>::build(store, compressor.name, dtype, chunk_memory_layout, shape, chunk_shape, full_path, chunk_separator, attrs, compressor_config, chunk_pool_size, fill_value, zarr_version_major);
     }
 
     template <class store_type>
-    zarray get_zarr_array(store_type store, const std::string& path, std::size_t chunk_pool_size, const std::size_t zarr_version_major = 3)
+    zarray get_zarr_array(store_type store, const std::string& path, std::size_t chunk_pool_size, const std::size_t zarr_version_major)
     {
         std::string s;
         nlohmann::json attrs;

diff --git a/include/xtensor-zarr/xzarr_group.hpp b/include/xtensor-zarr/xzarr_group.hpp
@@ -18,7 +18,7 @@ namespace xt
     class xzarr_group
     {
     public:
-        xzarr_group(store_type& store, const std::string& path);
+        xzarr_group(store_type& store, const std::string& path, const std::size_t zarr_version_major);
 
         xzarr_group create_group(const nlohmann::json& attrs=nlohmann::json::object(), const nlohmann::json& extensions=nlohmann::json::array());
 
@@ -29,27 +29,43 @@ namespace xt
         store_type& m_store;
         nlohmann::json m_json;
         std::string m_path;
+        std::size_t m_zarr_version_major;
     };
 
     template <class store_type>
-    xzarr_group<store_type>::xzarr_group(store_type& store, const std::string& path)
+    xzarr_group<store_type>::xzarr_group(store_type& store, const std::string& path, const std::size_t zarr_version_major)
         : m_store(store)
         , m_path(path)
+        , m_zarr_version_major(zarr_version_major)
     {
-        auto f = m_store["meta/root" + m_path + ".group.json"];
-        if (f.exists())
+        if (zarr_version_major == 3)
         {
-            m_json = nlohmann::json::parse(std::string(f));
+            auto f = m_store["meta/root" + m_path + ".group.json"];
+            if (f.exists())
+            {
+                m_json = nlohmann::json::parse(std::string(f));
+            }
         }
     }
 
     template <class store_type>
     xzarr_group<store_type> xzarr_group<store_type>::create_group(const nlohmann::json& attrs, const nlohmann::json& extensions)
     {
         m_json = nlohmann::json::object();
-        m_json["attributes"] = attrs;
-        m_json["extensions"] = extensions;
-        m_store["meta/root" + m_path + ".group.json"] = m_json.dump(4);
+        switch (m_zarr_version_major)
+        {
+            case 3:
+                m_json["attributes"] = attrs;
+                m_json["extensions"] = extensions;
+                m_store["meta/root" + m_path + ".group.json"] = m_json.dump(4);
+                break;
+            case 2:
+                m_json["zarr_format"] = 2;
+                m_store[m_path + ".zgroup"] = m_json.dump(4);
+                break;
+            default:
+                break;
+        }
         return *this;
     }
 

diff --git a/include/xtensor-zarr/xzarr_hierarchy.hpp b/include/xtensor-zarr/xzarr_hierarchy.hpp
@@ -114,26 +114,26 @@ namespace xt
     template <class store_type>
     xzarr_group<store_type> xzarr_hierarchy<store_type>::create_group(const std::string& path, const nlohmann::json& attrs, const nlohmann::json& extensions)
     {
-        xzarr_group<store_type> g(m_store, path);
+        xzarr_group<store_type> g(m_store, path, m_zarr_version_major);
         return g.create_group(attrs, extensions);
     }
 
     template <class store_type>
     xzarr_node<store_type> xzarr_hierarchy<store_type>::operator[](const std::string& path)
     {
-        return xzarr_node<store_type>(m_store, path);
+        return xzarr_node<store_type>(m_store, path, m_zarr_version_major);
     }
 
     template <class store_type>
     nlohmann::json xzarr_hierarchy<store_type>::get_children(const std::string& path)
     {
-        return xzarr_node<store_type>(m_store, path).get_children();
+        return xzarr_node<store_type>(m_store, path, m_zarr_version_major).get_children();
     }
 
     template <class store_type>
     nlohmann::json xzarr_hierarchy<store_type>::get_nodes(const std::string& path)
     {
-        return xzarr_node<store_type>(m_store, path).get_nodes();
+        return xzarr_node<store_type>(m_store, path, m_zarr_version_major).get_nodes();
     }
 
     /************************************

diff --git a/include/xtensor-zarr/xzarr_node.hpp b/include/xtensor-zarr/xzarr_node.hpp
@@ -35,7 +35,7 @@ namespace xt
     class xzarr_node
     {
     public:
-        xzarr_node(store_type& store, const std::string& path);
+        xzarr_node(store_type& store, const std::string& path, const std::size_t zarr_version_major);
 
         xzarr_group<store_type> create_group(const std::string& name, const nlohmann::json& attrs=nlohmann::json::object(), const nlohmann::json& extensions=nlohmann::json::array());
 
@@ -55,11 +55,13 @@ namespace xt
         nlohmann::json m_json;
         std::string m_path;
         xzarr_node_type m_node_type;
+        std::size_t m_zarr_version_major;
     };
 
     template <class store_type>
-    xzarr_node<store_type>::xzarr_node(store_type& store, const std::string& path)
+    xzarr_node<store_type>::xzarr_node(store_type& store, const std::string& path, const std::size_t zarr_version_major)
         : m_store(store)
+        , m_zarr_version_major(zarr_version_major)
     {
         m_path = path;
         if (m_path.front() != '/')
@@ -100,7 +102,7 @@ namespace xt
     xzarr_group<store_type> xzarr_node<store_type>::create_group(const std::string& name, const nlohmann::json& attrs, const nlohmann::json& extensions)
     {
         m_node_type = xzarr_node_type::explicit_group;
-        xzarr_group<store_type> g(m_store, m_path + '/' + name);
+        xzarr_group<store_type> g(m_store, m_path + '/' + name, m_zarr_version_major);
         return g.create_group(attrs, extensions);
     }
 
@@ -111,7 +113,7 @@ namespace xt
         {
             XTENSOR_THROW(std::runtime_error, "Node is not a group: " + m_path);
         }
-        xzarr_group<store_type> g(m_store, m_path);
+        xzarr_group<store_type> g(m_store, m_path, m_zarr_version_major);
         return g;
     }
 
@@ -120,7 +122,7 @@ namespace xt
     zarray xzarr_node<store_type>::create_array(const std::string& name, shape_type shape, shape_type chunk_shape, const std::string& dtype, O o)
     {
         m_node_type = xzarr_node_type::array;
-        return create_zarr_array(m_store, m_path + '/' + name, shape, chunk_shape, dtype, o.chunk_memory_layout, o.chunk_separator, o.compressor, o.attrs, o.chunk_pool_size, o.fill_value);
+        return create_zarr_array(m_store, m_path + '/' + name, shape, chunk_shape, dtype, o.chunk_memory_layout, o.chunk_separator, o.compressor, o.attrs, o.chunk_pool_size, o.fill_value, m_zarr_version_major);
     }
 
     template <class store_type>
@@ -130,7 +132,7 @@ namespace xt
         {
             XTENSOR_THROW(std::runtime_error, "Node is not an array: " + m_path);
         }
-        return get_zarr_array(m_store, m_path, chunk_pool_size);
+        return get_zarr_array(m_store, m_path, chunk_pool_size, m_zarr_version_major);
     }
 
     template <class store_type>
@@ -210,7 +212,7 @@ namespace xt
     template <class store_type>
     xzarr_node<store_type> xzarr_node<store_type>::operator[](const std::string& name)
     {
-        return xzarr_node<store_type>(m_store, m_path + '/' + name);
+        return xzarr_node<store_type>(m_store, m_path + '/' + name, m_zarr_version_major);
     }
 
     template <class store_type>