Support in place update of group members (#3928) (#3940)

This adds support for updating group members. We also modify the on disk format for a v2 group members in group details to facilitate the new updating support. A new API is not added in this PR but the act of removing and adding in the same group open is now supported. I've also reshuffled the code to add a new GroupDetails object which is a missing layer of abstraction from the previous group implementation. This separates the on-disk format (GroupDetails) from the overarching group class. --- TYPE: FEATURE DESC: Support in place update of group members Co-authored-by: Seth Shelnutt <[email protected]>
TileDB-Inc · Mar 3, 2023 · 1fb59c4 · 1fb59c4
1 parent 5b3d42d
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diff --git a/format_spec/group.md b/format_spec/group.md
@@ -1,6 +1,8 @@
 # Group
 
-A group consists of [metadata](./metadata.md) and a file containing group members
+A group consists of [metadata](./metadata.md) and a file containing group members.
+
+The current group format version is `2`.
 
 ```
 my_group                       # Group folder
@@ -24,7 +26,9 @@ my_group                       # Group folder
 
 ## Group Member
 
-The group member is the content inside a [group](./group.md)
+The group member is the content inside a [group](./group.md).
+
+The current group member format version is `2`.
 
 | **Field** | **Type** | **Description** |
 | :--- | :--- | :--- |
@@ -33,3 +37,4 @@ The group member is the content inside a [group](./group.md)
 | Relative | `uint8_t` | Is the URI relative to the group |
 | URI length | `uint32_t` | Number of characters in URI |
 | URI | `uint8_t[]` | URI character array |
+| Deleted | `uint8_t` | Is the member deleted |
diff --git a/test/src/unit-capi-group.cc b/test/src/unit-capi-group.cc
@@ -354,7 +354,7 @@ TEST_CASE_METHOD(
       tiledb_group_put_metadata(ctx_, group, "key", TILEDB_INT32, 1, &v);
   CHECK(rc == TILEDB_ERR);
 
-  // Write metadata on an group opened in READ mode
+  // Write metadata on a group opened in READ mode
   set_group_timestamp(group, 1);
   rc = tiledb_group_open(ctx_, group, TILEDB_READ);
   REQUIRE(rc == TILEDB_OK);
@@ -630,6 +630,99 @@ TEST_CASE_METHOD(
   remove_temp_dir(temp_dir);
 }
 
+TEST_CASE_METHOD(
+    GroupFx,
+    "C API: Group, write/read/update with named members",
+    "[capi][group][metadata][read]") {
+  // Create and open group in write mode
+  // TODO: refactor for each supported FS.
+  std::string temp_dir = fs_vec_[0]->temp_dir();
+  create_temp_dir(temp_dir);
+
+  const tiledb::sm::URI array1_uri(temp_dir + "array1");
+  const tiledb::sm::URI array2_uri(temp_dir + "array2");
+  create_array(array1_uri.to_string());
+  create_array(array2_uri.to_string());
+
+  tiledb::sm::URI group1_uri(temp_dir + "group1");
+  REQUIRE(tiledb_group_create(ctx_, group1_uri.c_str()) == TILEDB_OK);
+
+  // Set expected
+  std::vector<std::pair<tiledb::sm::URI, tiledb_object_t>> group1_expected = {
+      {array1_uri, TILEDB_ARRAY},
+  };
+
+  std::vector<std::pair<tiledb::sm::URI, tiledb_object_t>>
+      group1_expected_modified = {
+          {array2_uri, TILEDB_ARRAY},
+      };
+
+  tiledb_group_t* group1;
+  int rc = tiledb_group_alloc(ctx_, group1_uri.c_str(), &group1);
+  REQUIRE(rc == TILEDB_OK);
+  set_group_timestamp(group1, 1);
+  rc = tiledb_group_open(ctx_, group1, TILEDB_WRITE);
+  REQUIRE(rc == TILEDB_OK);
+
+  rc = tiledb_group_add_member(ctx_, group1, array1_uri.c_str(), false, "one");
+  REQUIRE(rc == TILEDB_OK);
+
+  // Close group from write mode
+  rc = tiledb_group_close(ctx_, group1);
+  REQUIRE(rc == TILEDB_OK);
+
+  // Reopen in read mode
+  rc = tiledb_group_open(ctx_, group1, TILEDB_READ);
+  REQUIRE(rc == TILEDB_OK);
+
+  uint8_t is_relative = 255;
+  rc = tiledb_group_get_is_relative_uri_by_name(
+      ctx_, group1, "one", &is_relative);
+  REQUIRE(rc == TILEDB_OK);
+  REQUIRE(is_relative == 0);
+
+  std::vector<std::pair<tiledb::sm::URI, tiledb_object_t>> group1_received =
+      read_group(group1);
+  REQUIRE_THAT(
+      group1_received, Catch::Matchers::UnorderedEquals(group1_expected));
+
+  // Close group
+  rc = tiledb_group_close(ctx_, group1);
+  REQUIRE(rc == TILEDB_OK);
+
+  // Remove assets from group
+  set_group_timestamp(group1, 2);
+  rc = tiledb_group_open(ctx_, group1, TILEDB_WRITE);
+  REQUIRE(rc == TILEDB_OK);
+
+  // Remove one
+  rc = tiledb_group_remove_member(ctx_, group1, "one");
+  REQUIRE(rc == TILEDB_OK);
+  // Add one back with different URI
+  rc = tiledb_group_add_member(ctx_, group1, array2_uri.c_str(), false, "one");
+  REQUIRE(rc == TILEDB_OK);
+
+  // Close group
+  rc = tiledb_group_close(ctx_, group1);
+  REQUIRE(rc == TILEDB_OK);
+
+  // Check read again
+  set_group_timestamp(group1, 2);
+  rc = tiledb_group_open(ctx_, group1, TILEDB_READ);
+  REQUIRE(rc == TILEDB_OK);
+
+  group1_received = read_group(group1);
+  REQUIRE_THAT(
+      group1_received,
+      Catch::Matchers::UnorderedEquals(group1_expected_modified));
+
+  // Close group
+  rc = tiledb_group_close(ctx_, group1);
+  REQUIRE(rc == TILEDB_OK);
+  tiledb_group_free(&group1);
+  remove_temp_dir(temp_dir);
+}
+
 TEST_CASE_METHOD(
     GroupFx,
     "C API: Group, write/read with named members",
@@ -1446,22 +1539,40 @@ TEST_CASE_METHOD(
   REQUIRE_THAT(
       group2_received, Catch::Matchers::UnorderedEquals(group2_expected));
 
+  // These tests are commented out because we need to introduce c-api
+  // serialization for the GroupUpdate structure
+  /*
   // Now that we validated the groups were written correctly
   // lets test taking a read, serializing it and writing
   rc = tiledb_group_alloc(ctx_, group3_uri.c_str(), &group3_write_deserialized);
   REQUIRE(rc == TILEDB_OK);
-  set_group_timestamp(group3_write_deserialized, 2);
+  set_group_timestamp(group3_write_deserialized, 3);
   rc = tiledb_group_open(ctx_, group3_write_deserialized, TILEDB_WRITE);
   REQUIRE(rc == TILEDB_OK);
 
+  // Setup serialized write with removed member
+  // Remove assets from group
+  tiledb_group_t* group3_write_setup;
+  rc = tiledb_group_alloc(ctx_, group3_uri.c_str(), &group3_write_setup);
+  REQUIRE(rc == TILEDB_OK);
+  set_group_timestamp(group3_write_setup, 2);
+  rc = tiledb_group_open(ctx_, group3_write_setup, TILEDB_WRITE);
+  REQUIRE(rc == TILEDB_OK);
+  rc = tiledb_group_remove_member(ctx_, group3_write_setup, group2_uri.c_str());
+  REQUIRE(rc == TILEDB_OK);
+
+  // Close so changes are applied
+  rc = tiledb_group_close(ctx_, group3_write_setup);
+
   rc = tiledb_group_serialize(
-      ctx_, group1_read, group3_write_deserialized, TILEDB_JSON);
+      ctx_, group3_write_setup, group3_write_deserialized, TILEDB_JSON);
   REQUIRE(rc == TILEDB_OK);
 
   // Close deserialized write group
   rc = tiledb_group_close(ctx_, group3_write_deserialized);
   REQUIRE(rc == TILEDB_OK);
   tiledb_group_free(&group3_write_deserialized);
+  tiledb_group_free(&group3_write_setup);
 
   rc = tiledb_group_alloc(ctx_, group4_uri.c_str(), &group4_write_deserialized);
   REQUIRE(rc == TILEDB_OK);
@@ -1479,30 +1590,33 @@ TEST_CASE_METHOD(
   tiledb_group_free(&group4_write_deserialized);
 
   // Check deserialized group3
-  set_group_timestamp(group3_read, 2);
+  set_group_timestamp(group3_read, 3);
   rc = tiledb_group_open(ctx_, group3_read, TILEDB_READ);
   REQUIRE(rc == TILEDB_OK);
   group3_received = read_group(group3_read);
   REQUIRE_THAT(
       group3_received, Catch::Matchers::UnorderedEquals(group3_expected));
 
   // Check deserialized group4
-  set_group_timestamp(group4_read, 2);
+  set_group_timestamp(group4_read, 3);
   rc = tiledb_group_open(ctx_, group4_read, TILEDB_READ);
   REQUIRE(rc == TILEDB_OK);
   group4_received = read_group(group4_read);
   REQUIRE_THAT(
       group4_received, Catch::Matchers::UnorderedEquals(group4_expected));
+ */
 
   // Close group
   rc = tiledb_group_close(ctx_, group1_read);
   REQUIRE(rc == TILEDB_OK);
   rc = tiledb_group_close(ctx_, group2_read);
   REQUIRE(rc == TILEDB_OK);
-  rc = tiledb_group_close(ctx_, group3_read);
-  REQUIRE(rc == TILEDB_OK);
-  rc = tiledb_group_close(ctx_, group4_read);
-  REQUIRE(rc == TILEDB_OK);
+  /*
+    rc = tiledb_group_close(ctx_, group3_read);
+    REQUIRE(rc == TILEDB_OK);
+    rc = tiledb_group_close(ctx_, group4_read);
+    REQUIRE(rc == TILEDB_OK);
+  */
   tiledb_group_free(&group1_read);
   tiledb_group_free(&group2_read);
   tiledb_group_free(&group3_read);

diff --git a/tiledb/CMakeLists.txt b/tiledb/CMakeLists.txt
@@ -209,10 +209,13 @@ set(TILEDB_CORE_SOURCES
   ${TILEDB_CORE_INCLUDE_DIR}/tiledb/sm/global_state/signal_handlers.cc
   ${TILEDB_CORE_INCLUDE_DIR}/tiledb/sm/global_state/watchdog.cc
   ${TILEDB_CORE_INCLUDE_DIR}/tiledb/sm/group/group.cc
+  ${TILEDB_CORE_INCLUDE_DIR}/tiledb/sm/group/group_details.cc
+  ${TILEDB_CORE_INCLUDE_DIR}/tiledb/sm/group/group_details_v1.cc
+  ${TILEDB_CORE_INCLUDE_DIR}/tiledb/sm/group/group_details_v2.cc
   ${TILEDB_CORE_INCLUDE_DIR}/tiledb/sm/group/group_directory.cc
   ${TILEDB_CORE_INCLUDE_DIR}/tiledb/sm/group/group_member.cc
   ${TILEDB_CORE_INCLUDE_DIR}/tiledb/sm/group/group_member_v1.cc
-  ${TILEDB_CORE_INCLUDE_DIR}/tiledb/sm/group/group_v1.cc
+  ${TILEDB_CORE_INCLUDE_DIR}/tiledb/sm/group/group_member_v2.cc
   ${TILEDB_CORE_INCLUDE_DIR}/tiledb/sm/metadata/metadata.cc
   ${TILEDB_CORE_INCLUDE_DIR}/tiledb/sm/misc/cancelable_tasks.cc
   ${TILEDB_CORE_INCLUDE_DIR}/tiledb/sm/misc/constants.cc

diff --git a/tiledb/api/c_api/group/group_api.cc b/tiledb/api/c_api/group/group_api.cc
@@ -34,7 +34,7 @@
 #include "tiledb/api/c_api_support/c_api_support.h"
 #include "tiledb/sm/c_api/tiledb_serialization.h"
 #include "tiledb/sm/enums/serialization_type.h"
-#include "tiledb/sm/group/group_v1.h"
+#include "tiledb/sm/group/group_details_v1.h"
 #include "tiledb/sm/serialization/array.h"
 #include "tiledb/sm/serialization/group.h"
 
@@ -95,7 +95,7 @@ capi_return_t tiledb_group_alloc(
   auto uri = tiledb::sm::URI(group_uri);
   if (uri.is_invalid()) {
     throw CAPIStatusException(
-        "Failed to create TileDB group object; Invalid URI");
+        "Failed to allocate TileDB group API object; Invalid URI");
   }
 
   *group = tiledb_group_handle_t::make_handle(uri, ctx->storage_manager());

diff --git a/tiledb/api/c_api/group/group_api_internal.h b/tiledb/api/c_api/group/group_api_internal.h
@@ -36,7 +36,6 @@
 #include "../../c_api_support/handle/handle.h"
 #include "../error/error_api_internal.h"
 #include "tiledb/sm/group/group.h"
-#include "tiledb/sm/group/group_v1.h"
 
 struct tiledb_group_handle_t
     : public tiledb::api::CAPIHandle<tiledb_group_handle_t> {
@@ -46,7 +45,7 @@ struct tiledb_group_handle_t
   static constexpr std::string_view object_type_name{"group"};
 
  private:
-  tiledb::sm::GroupV1 group_;
+  tiledb::sm::Group group_;
 
  public:
   tiledb_group_handle_t() = delete;
@@ -62,7 +61,7 @@ struct tiledb_group_handle_t
 
   [[nodiscard]] inline tiledb::sm::Group& group() const {
     return static_cast<tiledb::sm::Group&>(
-        const_cast<tiledb::sm::GroupV1&>(group_));
+        const_cast<tiledb::sm::Group&>(group_));
   }
 };
 

diff --git a/tiledb/sm/consolidator/group_meta_consolidator.cc b/tiledb/sm/consolidator/group_meta_consolidator.cc
@@ -35,7 +35,7 @@
 #include "tiledb/sm/enums/datatype.h"
 #include "tiledb/sm/enums/query_type.h"
 #include "tiledb/sm/group/group.h"
-#include "tiledb/sm/group/group_v1.h"
+#include "tiledb/sm/group/group_details_v1.h"
 #include "tiledb/sm/misc/parallel_functions.h"
 #include "tiledb/sm/stats/global_stats.h"
 #include "tiledb/sm/storage_manager/storage_manager.h"
@@ -75,12 +75,12 @@ Status GroupMetaConsolidator::consolidate(
 
   // Open group for reading
   auto group_uri = URI(group_name);
-  GroupV1 group_for_reads(group_uri, storage_manager_);
+  Group group_for_reads(group_uri, storage_manager_);
   RETURN_NOT_OK(group_for_reads.open(
       QueryType::READ, config_.timestamp_start_, config_.timestamp_end_));
 
   // Open group for writing
-  GroupV1 group_for_writes(group_uri, storage_manager_);
+  Group group_for_writes(group_uri, storage_manager_);
   RETURN_NOT_OK_ELSE(
       group_for_writes.open(QueryType::WRITE),
       throw_if_not_ok(group_for_reads.close()));

diff --git a/tiledb/sm/group/CMakeLists.txt b/tiledb/sm/group/CMakeLists.txt
@@ -34,7 +34,7 @@ include(common NO_POLICY_SCOPE)
 # linked standalone. As a result, this library is not defined with
 # `commence(object_library)`, since that mandates a link-completeness test.
 #
-add_library(group OBJECT group_directory.cc group.cc group_member.cc group_v1.cc group_member_v1.cc)
+add_library(group OBJECT group_directory.cc group.cc group_details.cc group_details_v1.cc group_details_v2.cc group_member.cc group_member_v1.cc group_member_v2.cc)
 target_link_libraries(group PUBLIC baseline $<TARGET_OBJECTS:baseline>)
 target_link_libraries(group PUBLIC buffer $<TARGET_OBJECTS:buffer>)