Correct filehandle use in VFS serialization

R/RcppExports.R

@@ -954,6 +954,10 @@ libtiledb_vfs_copy_file <- function(vfs, old_uri, new_uri) {
     .Call(`_tiledb_libtiledb_vfs_copy_file`, vfs, old_uri, new_uri)
 }
 
+libtiledb_vfs_fh_free <- function(fhxp) {
+    invisible(.Call(`_tiledb_libtiledb_vfs_fh_free`, fhxp))
+}
+
 libtiledb_stats_enable <- function() {
     invisible(.Call(`_tiledb_libtiledb_stats_enable`))
 }

R/VFS.R

@@ -394,9 +394,10 @@ tiledb_vfs_unserialize <- function(uri, vfs = tiledb_get_vfs()) {
     stopifnot("Argument 'vfs' must a tiledb_vfs object" = is(vfs, "tiledb_vfs"),
               "Argument 'uri' must be character" = is.character(uri))
     n <- tiledb_vfs_file_size(uri)
-    file <- tiledb_vfs_open(uri, "READ")
-    vec <- tiledb_vfs_read(file, 0, n)
-    tiledb_vfs_close(file)
+    fh <- tiledb_vfs_open(uri, "READ")
+    vec <- tiledb_vfs_read(fh, 0, n)
+    tiledb_vfs_close(fh)
+    libtiledb_vfs_fh_free(fh)
     ## The gzcon(rawConnection()) idea is from https://stackoverflow.com/a/58136567/508431
     ## The packBits(intToBits()) part on the int vector read is from a friend via slack
     obj <- unserialize(gzcon(rawConnection(packBits(intToBits(vec)))))
@@ -420,15 +421,17 @@ tiledb_vfs_serialize <- function(obj, uri, vfs = tiledb_get_vfs()) {
     saveRDS(obj, tf)
 
     ## Read local file
-    file <- tiledb_vfs_open(tf, "READ")
-    vec <- tiledb_vfs_read(file, 0, tiledb_vfs_file_size(tf))
-    tiledb_vfs_close(file)
+    fh <- tiledb_vfs_open(tf, "READ")
+    vec <- tiledb_vfs_read(fh, 0, tiledb_vfs_file_size(tf))
+    tiledb_vfs_close(fh)
+    libtiledb_vfs_fh_free(fh)
 
     ## Now write 'vec' to the target URI
-    file <- tiledb_vfs_open(uri, "WRITE")
-    tiledb_vfs_write(file, vec)
-    tiledb_vfs_sync(file)
-    tiledb_vfs_close(file)
+    fh <- tiledb_vfs_open(uri, "WRITE")
+    tiledb_vfs_write(fh, vec)
+    tiledb_vfs_sync(fh)
+    tiledb_vfs_close(fh)
+    libtiledb_vfs_fh_free(fh)
 
     unlink(tf)
     invisible(uri)

inst/include/tiledb.h

@@ -76,7 +76,11 @@ typedef std::unordered_map<std::string, std::shared_ptr<tiledb::ColumnBuffer>> m
 
 // C++ compiler complains about missing delete functionality when we use tiledb_vfs_fh_t directly
 struct vfs_fh {
-   void *fh;
+#if TILEDB_VERSION_MAJOR == 2 && TILEDB_VERSION_MINOR >= 15
+    tiledb_vfs_fh_handle_t* fh;
+#else
+    tiledb_vfs_fh_t* fh;
+#endif
 };
 typedef struct vfs_fh vfs_fh_t;
 

src/RcppExports.cpp

@@ -2847,6 +2847,16 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// libtiledb_vfs_fh_free
+void libtiledb_vfs_fh_free(XPtr<vfs_fh_t> fhxp);
+RcppExport SEXP _tiledb_libtiledb_vfs_fh_free(SEXP fhxpSEXP) {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< XPtr<vfs_fh_t> >::type fhxp(fhxpSEXP);
+    libtiledb_vfs_fh_free(fhxp);
+    return R_NilValue;
+END_RCPP
+}
 // libtiledb_stats_enable
 void libtiledb_stats_enable();
 RcppExport SEXP _tiledb_libtiledb_stats_enable() {
@@ -3783,6 +3793,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_tiledb_libtiledb_vfs_dir_size", (DL_FUNC) &_tiledb_libtiledb_vfs_dir_size, 2},
     {"_tiledb_libtiledb_vfs_ls", (DL_FUNC) &_tiledb_libtiledb_vfs_ls, 2},
     {"_tiledb_libtiledb_vfs_copy_file", (DL_FUNC) &_tiledb_libtiledb_vfs_copy_file, 3},
+    {"_tiledb_libtiledb_vfs_fh_free", (DL_FUNC) &_tiledb_libtiledb_vfs_fh_free, 1},
     {"_tiledb_libtiledb_stats_enable", (DL_FUNC) &_tiledb_libtiledb_stats_enable, 0},
     {"_tiledb_libtiledb_stats_disable", (DL_FUNC) &_tiledb_libtiledb_stats_disable, 0},
     {"_tiledb_libtiledb_stats_reset", (DL_FUNC) &_tiledb_libtiledb_stats_reset, 0},

src/libtiledb.cpp

@@ -4324,11 +4324,15 @@ XPtr<vfs_fh_t> libtiledb_vfs_open(XPtr<tiledb::Context> ctxxp, XPtr<tiledb::VFS>
   check_xptr_tag<tiledb::VFS>(vfsxp);
   std::shared_ptr<tiledb_ctx_t> ctx = ctxxp.get()->ptr();
   std::shared_ptr<tiledb_vfs_t> vfs = vfsxp.get()->ptr();
+#if TILEDB_VERSION >= TileDB_Version(2,15,0)
+  tiledb_vfs_fh_handle_t *fh = nullptr;
+#else
   tiledb_vfs_fh_t *fh = nullptr;
+#endif
   tiledb_vfs_mode_t vfsmode = _string_to_tiledb_vfs_mode_t(mode);
   tiledb_vfs_open(ctx.get(), vfs.get(), uri.c_str(), vfsmode, &fh);
   XPtr<vfs_fh_t> ptr = make_xptr<vfs_fh_t>(new vfs_fh_t);
-  ptr->fh = static_cast<void*>(fh);
+  ptr->fh = fh;
   return ptr;
 }
 
@@ -4337,7 +4341,7 @@ void libtiledb_vfs_close(XPtr<tiledb::Context> ctxxp, XPtr<vfs_fh_t> fh) {
   check_xptr_tag<tiledb::Context>(ctxxp);
   check_xptr_tag<vfs_fh_t>(fh);
   std::shared_ptr<tiledb_ctx_t> ctx = ctxxp.get()->ptr();
-  tiledb_vfs_close(ctx.get(), static_cast<tiledb_vfs_fh_t*>(fh->fh));
+  tiledb_vfs_close(ctx.get(), fh->fh);
 }
 
 // [[Rcpp::export]]
@@ -4346,8 +4350,7 @@ void libtiledb_vfs_write(XPtr<tiledb::Context> ctxxp, XPtr<vfs_fh_t> fh,
   check_xptr_tag<tiledb::Context>(ctxxp);
   check_xptr_tag<vfs_fh_t>(fh);
   std::shared_ptr<tiledb_ctx_t> ctx = ctxxp.get()->ptr();
-  tiledb_vfs_write(ctx.get(), static_cast<tiledb_vfs_fh_t*>(fh->fh),
-                   &(vec[0]), vec.size()*sizeof(int));
+  tiledb_vfs_write(ctx.get(), fh->fh, &(vec[0]), vec.size()*sizeof(int));
 }
 
 // [[Rcpp::export]]
@@ -4359,7 +4362,7 @@ Rcpp::IntegerVector libtiledb_vfs_read(XPtr<tiledb::Context> ctxxp, XPtr<vfs_fh_
   std::int64_t offs = fromInteger64(offset);
   std::int64_t nb = fromInteger64(nbytes);
   Rcpp::IntegerVector buf(nb/4);
-  tiledb_vfs_read(ctx.get(), static_cast<tiledb_vfs_fh_t*>(fh->fh), offs, &(buf[0]), nb);
+  tiledb_vfs_read(ctx.get(), fh->fh, offs, &(buf[0]), nb);
   return buf;
 }
 
@@ -4368,7 +4371,7 @@ void libtiledb_vfs_sync(XPtr<tiledb::Context> ctxxp, XPtr<vfs_fh_t> fh) {
   check_xptr_tag<tiledb::Context>(ctxxp);
   check_xptr_tag<vfs_fh_t>(fh);
   std::shared_ptr<tiledb_ctx_t> ctx = ctxxp.get()->ptr();
-  tiledb_vfs_sync(ctx.get(), static_cast<tiledb_vfs_fh_t*>(fh->fh));
+  tiledb_vfs_sync(ctx.get(), fh->fh);
 }
 
 // [[Rcpp::export]]
@@ -4390,6 +4393,17 @@ std::string libtiledb_vfs_copy_file(XPtr<tiledb::VFS> vfs, std::string old_uri,
     return new_uri;
 }
 
+// [[Rcpp::export]]
+void libtiledb_vfs_fh_free(XPtr<vfs_fh_t> fhxp) {
+    check_xptr_tag<vfs_fh_t>(fhxp);
+    spdl::trace("[libtiledb_vfs_clear_handle] entered");
+    vfs_fh_t* strptr = fhxp.get();
+#if TILEDB_VERSION >= TileDB_Version(2,15,0)
+    tiledb_vfs_fh_handle_t *fh = strptr->fh;
+    tiledb_vfs_fh_free(&fh);
+#endif
+}
+
 /**
  * Stats
  */