Do not create empty .vac files in metadata consolidation (#5453)

When we are trying to consolidate array or group metadata but there are
no array or group metadata present, we are creating an empty `.vac` file
on local filesystems. In object stores, notably on S3 that I have
tested, our `write` method currently doesn't create a file when size is
`0` (this is most probably another issue to fix), so we don't observe
the same behavior.

This PR unifies the behavior by enforcing that we don't create a `.vac`
file if no consolidation is possible, aka if there are 0 or 1
array/group metadata present. We already do such a check for fragment
metadata, fragments and commit consolidation.
Both tests in this PR were failing without the fix and are now passing.

---
TYPE: BUG
DESC: Do not create empty .vac files in metadata consolidation

Author: ypatia

test/src/unit-capi-consolidation.cc

@@ -7895,3 +7895,48 @@ TEST_CASE_METHOD(
     remove_sparse_array();
   }
 }
+
+TEST_CASE_METHOD(
+    ConsolidationFx,
+    "C API: Test consolidating empty array metadata",
+    "[capi][consolidation][array-meta][empty][sc-62900][non-rest]") {
+  remove_dense_array();
+  create_dense_array();
+
+  SECTION("Consolidate empty array metadata") {
+    // Configuration for consolidating array metadata
+    tiledb_config_t* config = nullptr;
+    tiledb_error_t* error = nullptr;
+    REQUIRE(tiledb_config_alloc(&config, &error) == TILEDB_OK);
+    REQUIRE(error == nullptr);
+    int rc = tiledb_config_set(
+        config, "sm.consolidation.mode", "array_meta", &error);
+    REQUIRE(rc == TILEDB_OK);
+    REQUIRE(error == nullptr);
+
+    // Consolidate without having added any array meta
+    rc = tiledb_array_consolidate(ctx_, dense_array_uri_.c_str(), config);
+    CHECK(rc == TILEDB_OK);
+
+    // We must have 0 vacuum files after consolidation.
+    std::vector<std::string> array_meta_vac_files;
+    get_array_meta_vac_files_dense(array_meta_vac_files);
+    CHECK(array_meta_vac_files.size() == 0);
+
+    tiledb_array_t* array;
+    rc = tiledb_array_alloc(ctx_, dense_array_uri_.c_str(), &array);
+    REQUIRE(rc == TILEDB_OK);
+
+    // Open for Delete, so that array metadata are loaded from disk, and check
+    // there is no failure
+    rc = tiledb_array_open(ctx_, array, TILEDB_DELETE);
+    REQUIRE(rc == TILEDB_OK);
+
+    // Vacuum consolidated array metadata (empty) and check there is no failure
+    rc = tiledb_config_set(config, "sm.vacuum.mode", "array_meta", &error);
+    REQUIRE(rc == TILEDB_OK);
+    REQUIRE(error == nullptr);
+    rc = tiledb_array_vacuum(ctx_, dense_array_uri_.c_str(), config);
+    CHECK(rc == TILEDB_OK);
+  }
+}

test/src/unit-capi-group.cc

@@ -1083,6 +1083,19 @@ TEST_CASE_METHOD(
   tiledb::sm::URI group_uri(temp_dir + "group");
   REQUIRE(tiledb_group_create(ctx_, group_uri.c_str()) == TILEDB_OK);
 
+  // Consolidate empty metadata
+  tiledb_config_t* cfg;
+  tiledb_error_t* err = nullptr;
+  REQUIRE(tiledb_config_alloc(&cfg, &err) == TILEDB_OK);
+  int rc = tiledb_group_consolidate_metadata(ctx_, group_uri.c_str(), cfg);
+  REQUIRE(rc == TILEDB_OK);
+
+  // Check no .vac file is created
+  std::vector<std::string> group_empty_meta_vac_files;
+  get_meta_vac_files(group_uri, group_empty_meta_vac_files);
+  CHECK(group_empty_meta_vac_files.size() == 0);
+  tiledb_config_free(&cfg);
+
   write_group_metadata(group_uri.c_str());
   std::this_thread::sleep_for(std::chrono::milliseconds(1));
   auto start = tiledb::sm::utils::time::timestamp_now_ms();
@@ -1100,7 +1113,7 @@ TEST_CASE_METHOD(
   CHECK(group_meta_files.size() == 4);
 
   uint64_t file_size = 0;
-  int rc = tiledb_vfs_file_size(
+  rc = tiledb_vfs_file_size(
       ctx_, vfs_, group_meta_vac_files[0].c_str(), &file_size);
   REQUIRE(rc == TILEDB_OK);
 

tiledb/sm/consolidator/array_meta_consolidator.cc

@@ -80,6 +80,12 @@ Status ArrayMetaConsolidator::consolidate(
       encryption_key,
       key_length));
 
+  // Check if there's actually more than 1 file to consolidate
+  auto& metadata_r = array_for_reads.metadata();
+  if (metadata_r.loaded_metadata_uris().size() <= 1) {
+    return Status::Ok();
+  }
+
   // Open array for writing
   Array array_for_writes(resources_, array_uri);
   RETURN_NOT_OK_ELSE(
@@ -88,7 +94,6 @@ Status ArrayMetaConsolidator::consolidate(
       throw_if_not_ok(array_for_reads.close()));
 
   // Copy-assign the read metadata into the metadata of the array for writes
-  auto& metadata_r = array_for_reads.metadata();
   array_for_writes.opened_array()->metadata() = metadata_r;
   URI new_uri = metadata_r.get_uri(array_uri);
   const auto& to_vacuum = metadata_r.loaded_metadata_uris();

tiledb/sm/consolidator/group_meta_consolidator.cc

@@ -83,8 +83,13 @@ Status GroupMetaConsolidator::consolidate(
     group_for_reads.close();
   }
 
-  // Copy-assign the read metadata into the metadata of the group for writes
+  // Check if there's actually more than 1 file to consolidate
   auto metadata_r = group_for_reads.metadata();
+  if (metadata_r->loaded_metadata_uris().size() <= 1) {
+    return Status::Ok();
+  }
+
+  // Copy-assign the read metadata into the metadata of the group for writes
   *(group_for_writes.metadata()) = *metadata_r;
   URI new_uri = metadata_r->get_uri(group_uri);
   const auto& to_vacuum = metadata_r->loaded_metadata_uris();